ALPL encodes tissue-nonspecific alkaline phosphatase (TNAP), a glycosylated, metal-dependent homodimer that commonly acts as a GPI-anchored ectoenzyme on cell surfaces and mineralizing matrix vesicles. Its active site contains zinc and magnesium, with a separate structural calcium site. TNAP hydrolyzes extracellular inorganic pyrophosphate, removing an inhibitor of hydroxyapatite propagation, and also releases phosphate from nucleotides. These activities support skeletal and dental mineralization. It dephosphorylates pyridoxal 5'-phosphate to pyridoxal, supporting cellular vitamin B6 availability, and hydrolyzes phosphocholine and phosphoethanolamine in recombinant human enzyme, serum and cell-based assays. The latter reactions supply choline and ethanolamine; mouse studies connect their perturbation to hepatic lipid metabolism. Recombinant human TNAP also hydrolyzes phosphocreatine. A mitochondrial TNAP pool drives phosphocreatine turnover and the futile creatine cycle in mouse thermogenic adipocytes, while direct human tissue targeting remains less well resolved. Loss-of-function ALPL variants cause hypophosphatasia with defective mineralization and, in severe cases, vitamin B6-related neurological manifestations. Increased TNAP activity can promote pathological soft-tissue calcification.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004035 alkaline phosphatase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved alkaline phosphatase chemistry is supported by the actual PAINT ancestral assertion and human enzyme assays. Reason: The cached PTHR11596 PAINT table places GO:0004035 at PTN000174527. Human P05186 is legitimately among its experimental descendants, rather than a circular transfer. Human recombinant TNAP substrate assays support retention of this broad catalytic function; no target-specific loss is evident. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000174527 SUPPORTS TRANSFER Exact IBD and descendant evidence inspected in interpro/panther/PTHR11596/PTHR11596-paint.tsv; independent human biological support is described in the reason. Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Plasma-membrane TNAP is an experimentally supported human ectoenzyme. Reason: The cached PAINT table places this assertion at PTN000904735. Human fibroblast membrane-impermeable substrate assays, extracellular acid inactivation and PI-PLC release independently corroborate the location. Preserve this phylogenetic assertion at its existing resolution; the directly assayed face is represented by refinement of the PMID:2220817 row. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000904735 SUPPORTS TRANSFER Exact IBD and descendant evidence inspected in interpro/panther/PTHR11596/PTHR11596-paint.tsv; independent human biological support is described in the reason. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0030282 bone mineralization | IBA GO_REF:0000033 | ACCEPT | Summary: TNAP performs phosphate chemistry required for skeletal mineral deposition. Reason: PTN002613308 carries the cached bone-mineralization IBD, supported there by mouse Alpl and zebrafish alpl. Human P05186 is not in this particular donor list; independent human hypophosphatasia genetics and enzyme chemistry nevertheless support the inherited function. PPi hydrolysis removes an inhibitor of crystal propagation, establishing participation beyond disease necessity alone. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002613308 SUPPORTS TRANSFER Exact IBD and descendant evidence inspected in interpro/panther/PTHR11596/PTHR11596-paint.tsv; independent human biological support is described in the reason. Supporting Evidence: PMID:9781036 Hypophosphatasia is an inherited disorder characterised by defective bone mineralisation and deficiency of serum and tissue liver/bone/kidney alkaline phosphatase (L/B/K ALP) activity. PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0004035 alkaline phosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Alkaline phosphatase activity is directly measured for human TNAP. Reason: Recombinant human TNAP hydrolyzes pNPP and physiological phosphoester substrates. The general alkaline phosphatase term captures a broad substrate repertoire rather than a single exclusive reaction; the more specific substrate rows add complementary coverage. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0004427 inorganic diphosphate phosphatase activity | IEA GO_REF:0000116 | ACCEPT | Summary: TNAP hydrolyzes inorganic diphosphate to phosphate. Reason: The RHEA:24576 chemistry agrees with assays of purified human TNAP and hypophosphatasia variants at physiological pH. Removing extracellular PPi promotes hydroxyapatite propagation; this is a principal mineralization mechanism, alongside nucleotide-derived Pi supply. Propagation Review Root cause: NO FAILURE CORE Sources checked: RHEA:24576 SUPPORTS TRANSFER Proximate machine source is preserved. The actual donor, reaction mapping or family scope and independent target evidence are distinguished in the reason. Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0005758 mitochondrial intermembrane space | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Mouse thermogenic adipocytes provide positive mitochondrial-localization evidence. Reason: PMID:33981039 directly localizes endogenous and tagged mouse TNAP to thermogenic-adipocyte mitochondria, using knockout-controlled imaging, fractionation, protease protection and APEX2. The construct is mouse P09242 and the tissue experiments are murine. Retain the conserved, tissue-restricted localization as non-core here; direct human recombinant phosphocreatine hydrolysis in the same paper does not by itself establish human mitochondrial targeting. This is a model boundary, not evidence of contamination or impossibility for a GPI-anchored protein. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: TNAP acts at the cell surface as a GPI-anchored ectophosphatase. Reason: The combined automatic subcellular-location and mouse-ortholog sources agree with independent human fibroblast topology assays. No finer location is required to retain this correct electronic membrane assertion. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0008253 5'-nucleotidase activity | IEA GO_REF:0000116 | ACCEPT | Summary: 5'-nucleotide dephosphorylation is part of TNAP's extracellular phosphate-releasing repertoire. Reason: RHEA:29375 specifies AMP hydrolysis. PMID:19874193 describes AMPase assays and demonstrates sequential nucleotide breakdown to adenosine and Pi in mouse matrix vesicles, with a strong TNAP-genotype dependence. The human UniProt reaction and measured human alkaline-phosphatase repertoire support the mapping. The human recombinant ATP/ADP kinetics and mouse vesicle AMP-flux experiments are distinct; no claim of universal dominance over NT5E is made. Propagation Review Root cause: NO FAILURE CORE Sources checked: RHEA:29375 SUPPORTS TRANSFER Proximate machine source is preserved. The actual donor, reaction mapping or family scope and independent target evidence are distinguished in the reason. Supporting Evidence: PMID:19874193 ATPase, pyrophosphatase (PPiase), ADPase, and AMPase activities were assayed discontinuously by measuring the amount of inorganic phosphate liberated PMID:19874193 A soluble epitope tagged from of human TNAP was produced and purified as described previously. |
| GO:0016791 phosphatase activity | IEA GO_REF:0000002 | MODIFY | Summary: The InterPro-derived phosphatase term can be refined to the established alkaline phosphatase activity. Reason: IPR001952/IPR018299 identify the alkaline-phosphatase family/signature, and human substrate assays establish the named subclass. The general phosphatase assertion is true but less informative for this family; refine its scope without alleging a propagation failure. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: InterPro:IPR001952 SUPPORTS TRANSFER Proximate machine source is preserved. The actual donor, reaction mapping or family scope and independent target evidence are distinguished in the reason. Proposed replacements: alkaline phosphatase activity Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | MODIFY | Summary: Human TNAP directly hydrolyzes ATP, but the present GO ATP-hydrolysis term carries an energy-coupling convention. Reason: PMID:19874193 measures ATP-to-ADP/Pi hydrolysis by soluble human TNAP at pH 7.4, alongside mouse matrix-vesicle experiments. Live GO:0016887 has a comment restricting usage to ATP-powered reactions and a part_of relation to ATP-dependent activity. No mechanical or chemical coupling of ATP energy is shown here. Refine to the immediate reaction parent GO:0017111, whose definition includes hydrolysis of a ribonucleoside triphosphate without that restriction. ATP is the measured substrate; this does not assert that every NTP is hydrolyzed. Preserve the positive chemistry and original source rather than reclassifying it as weak incidental activity. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: RHEA:13065 SUPPORTS TRANSFER Proximate machine source is preserved. The actual donor, reaction mapping or family scope and independent target evidence are distinguished in the reason. Proposed replacements: ribonucleoside triphosphate phosphatase activity Supporting Evidence: PMID:19874193 A soluble epitope tagged from of human TNAP was produced and purified as described previously. PMID:19874193 ATPase, pyrophosphatase (PPiase), ADPase, and AMPase activities were assayed discontinuously by measuring the amount of inorganic phosphate liberated |
| GO:0031966 mitochondrial membrane | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Mouse thermogenic adipocytes provide positive mitochondrial-localization evidence. Reason: PMID:33981039 directly localizes endogenous and tagged mouse TNAP to thermogenic-adipocyte mitochondria, using knockout-controlled imaging, fractionation, protease protection and APEX2. The construct is mouse P09242 and the tissue experiments are murine. Retain the conserved, tissue-restricted localization as non-core here; direct human recombinant phosphocreatine hydrolysis in the same paper does not by itself establish human mitochondrial targeting. This is a model boundary, not evidence of contamination or impossibility for a GPI-anchored protein. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0033883 pyridoxal phosphatase activity | IEA GO_REF:0000116 | ACCEPT | Summary: TNAP dephosphorylates extracellular pyridoxal phosphate. Reason: Human fibroblast ectoenzyme experiments and purified recombinant human TNAP substrate-selectivity measurements establish this catalytic step. It converts extracellular PLP to membrane-permeant pyridoxal, supporting vitamin B6 availability. Distinct mutant substrate effects are measured, but those biochemical differences alone do not assign a clinical seizure phenotype to each variant. Propagation Review Root cause: NO FAILURE CORE Sources checked: RHEA:20533 SUPPORTS TRANSFER Proximate machine source is preserved. The actual donor, reaction mapping or family scope and independent target evidence are distinguished in the reason. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0043262 ADP phosphatase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Human TNAP catalyzes ADP dephosphorylation as part of local Pi generation. Reason: RHEA:61436 and GO:0043262 specify ADP-to-AMP/Pi hydrolysis, without an energy-coupling requirement. PMID:19874193 directly assays recombinant human TNAP with ADP at pH 7.4 and separately analyzes nucleotide turnover in mouse matrix vesicles. This is a supported catalytic component of the mineralization-associated substrate repertoire. Propagation Review Root cause: NO FAILURE CORE Sources checked: RHEA:61436 SUPPORTS TRANSFER Proximate machine source is preserved. The actual donor, reaction mapping or family scope and independent target evidence are distinguished in the reason. Supporting Evidence: PMID:19874193 A soluble epitope tagged from of human TNAP was produced and purified as described previously. PMID:19874193 ATPase, pyrophosphatase (PPiase), ADPase, and AMPase activities were assayed discontinuously by measuring the amount of inorganic phosphate liberated |
| GO:0050187 phosphoamidase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Phosphocreatine hydrolysis is directly measured for recombinant human TNAP. Reason: PMID:33981039 explicitly assays commercial recombinant human TNAP with phosphocreatine at 37 degrees C and pH 7.8, deriving substrate kinetics. GO:0050187 has exactly the phosphocreatine-to-creatine/Pi reaction (RHEA:12977), despite the broad-sounding phosphoamidase label. Thus the human chemistry is not supported only by mouse similarity. Mouse adipocyte localization and thermogenic physiology remain separately scoped. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:33981039 recombinant human TNAP hydrolyzes PCr robustly (Extended Data Fig. 1e–g). |
| GO:0005576 extracellular region | IEA GO_REF:0000107 | ACCEPT | Summary: Extracellular TNAP includes an enzymatically active soluble pool. Reason: GPI-anchor release and circulating TNAP are compatible with this broad compartment. PMID:41145834 measures TNAP-sensitive phosphocholine and phosphoethanolamine hydrolysis in serum from six human donors at physiological pH, giving functional evidence beyond passive release. The Reactome source describes GPLD1 acting on a GPI-anchored protein; it does not make ALPL the GPI-cleaving enzyme, and its generic cached summary alone does not resolve an ALPL-specific entity. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0006580 ethanolamine metabolic process | IEA GO_REF:0000107 | ACCEPT | Summary: TNAP directly releases ethanolamine and choline from their phosphorylated precursors. Reason: The inherited mouse metabolic-process assertions are corroborated by recombinant human TNAP kinetics, human serum and HuH-6 cell-surface hydrolysis in PMID:41145834, and human fibroblast PEA hydrolysis in PMID:2220817. ALPL performs a chemical step in these processes. Mouse liver/plasma lipid phenotypes and human-cell growth rescue support physiological context, but do not establish a direct TNAP lipid-transport activity or a measured human VLDL secretion flux. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0016462 pyrophosphatase activity | IEA GO_REF:0000107 | MODIFY | Summary: The broad acid-anhydride hydrolase annotation can be made substrate-specific. Reason: The inherited mineralization assertion and PMID:12162492 substrate experiments specifically support inorganic PPi hydrolysis. Refine to GO:0004427. This refinement does not deny ATP/ADP hydrolysis established independently; GO:0016462 is a broad parent that includes several anhydride substrates. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Proposed replacements: inorganic diphosphate phosphatase activity Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0019695 choline metabolic process | IEA GO_REF:0000107 | ACCEPT | Summary: TNAP directly releases ethanolamine and choline from their phosphorylated precursors. Reason: The inherited mouse metabolic-process assertions are corroborated by recombinant human TNAP kinetics, human serum and HuH-6 cell-surface hydrolysis in PMID:41145834, and human fibroblast PEA hydrolysis in PMID:2220817. ALPL performs a chemical step in these processes. Mouse liver/plasma lipid phenotypes and human-cell growth rescue support physiological context, but do not establish a direct TNAP lipid-transport activity or a measured human VLDL secretion flux. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0030282 bone mineralization | IEA GO_REF:0000107 | ACCEPT | Summary: Conserved TNAP phosphatase chemistry supports bone mineralization. Reason: Mouse Alpl genetic/biochemical studies and direct human TNAP enzymology agree with human hypophosphatasia. TNAP consumes the mineralization inhibitor PPi and supplies Pi from extracellular substrates; the product therefore performs part of the mineralization process rather than serving only as a disease marker. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:9781036 Hypophosphatasia is an inherited disorder characterised by defective bone mineralisation and deficiency of serum and tissue liver/bone/kidney alkaline phosphatase (L/B/K ALP) activity. PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0031012 extracellular matrix | IEA GO_REF:0000107 | ACCEPT | Summary: TNAP operates at the extracellular mineralizing matrix and matrix-vesicle interface. Reason: The mouse-derived broad extracellular-matrix location is consistent with the established extracellular PPi-removal mechanism, vesicle-associated activity and human skeletal phenotype. Being GPI-anchored on matrix vesicles is compatible with action in the extracellular matrix; this is not evidence that TNAP is a soluble structural matrix protein. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:9781036 Hypophosphatasia is an inherited disorder characterised by defective bone mineralisation and deficiency of serum and tissue liver/bone/kidney alkaline phosphatase (L/B/K ALP) activity. PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0032496 response to lipopolysaccharide | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Rat pulmonary TNAP activity responds to endotoxin in a defined surfactant compartment. Reason: The MGI comparative Alpl graph traces the rat donor to PMID:11810315. Its primary abstract reports increased TNAP and intestinal-AP activities in heavy surfactant after LPS, while TNAP mRNA was not induced. Retain the context-specific response rather than equating it with TNAP transcriptional induction or direct LPS dephosphorylation. The human transfer is not a newly demonstrated human pulmonary assay. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:11810315 LPS instillation induced IAP-I mRNA, but not IAP-II mRNA or TNAP mRNA. |
| GO:0032868 response to insulin | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Insulin treatment reverses altered bone alkaline-phosphatase expression/activity in diabetic rats. Reason: The term-specific rat donor trace resolves to PMID:20818503. Its primary abstract describes streptozotocin diabetes, reduced bone ALP expression/activity and reversal with insulin. This supports a contextual response, not insulin-receptor activity or an intrinsic insulin-signaling enzyme role for ALPL. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:20818503 These changes in the bone of STZ-induced diabetic rats were reversed by insulin-treatment. |
| GO:0034516 response to vitamin B6 | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Vitamin B6 dependence and supplementation responses are documented in Tnap-deficient mice. Reason: The MGI mouse donor trace includes PMID:7550313, whose abstract reports abnormal PLP/GABA biology and rescue with pyridoxal plus a modified diet. Retain the contextual response annotation with this model boundary; ALPL catalytic participation in PLP metabolism is captured independently by the substrate-specific MF and process rows. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0036005 response to macrophage colony-stimulating factor | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: CSF-1 treatment changes alkaline-phosphatase expression in toothless osteopetrotic rats. Reason: The MGI rat donor trace resolves to PMID:7669437. Its independently indexed primary PubMed abstract reports Northern-blot normalization of osteoblast alkaline-phosphatase mRNA following CSF-1 treatment. The authors interpret this as correction of the osteopetrotic environment; it does not establish direct CSF-1 receptor signaling in ALPL or osteoblasts. Retain the measured contextual expression response without claiming a direct human experiment. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:7669437 While osteoblast-related gene expression as reflected by mRNA levels of alkaline phosphatase, osteocalcin, osteopontin, and type I collagen was normalized |
| GO:0042822 pyridoxal 5'-phosphate metabolic process | IEA GO_REF:0000107 | ACCEPT | Summary: ALPL directly catalyzes a step of pyridoxal-phosphate metabolism. Reason: Human fibroblasts and purified human TNAP establish PLP dephosphorylation; the mouse transfer is supported by this independent target chemistry. This is participation through catalysis, not an inference solely from vitamin-responsive seizures. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0051384 response to glucocorticoid | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Dexamethasone regulates tissue-specific rat alkaline-phosphatase transcription. Reason: The MGI rat donor trace resolves to PMID:2039500. The primary abstract reports inducible expression from alternative rat promoters, with increased upstream-promoter transcript and alkaline-phosphatase activity in ROS17/2.8 cells. This supports the contextual response term; ALPL is not thereby a glucocorticoid receptor or transcriptional regulator. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:2039500 the increase in ALP activity and mRNA levels following dexamethasone treatment of ROS17/2.8 cells is correlated with an increase in the level of transcripts from the upstream promoter. |
| GO:0052731 phosphocholine phosphatase activity | IEA GO_REF:0000107 | ACCEPT | Summary: Human TNAP directly hydrolyzes phosphocholine and phosphoethanolamine. Reason: PMID:41145834 assays purified human TNAP residues 18–500 expressed in Expi293F cells (kinetics at pH 9.0), human serum from six donors and HuH-6 surface hydrolysis at pH 7.4. These experiments support the substrate chemistry. PC/PEA poses are docking predictions, while the experimental structures contain phosphate or inhibitor; the catalytic claim rests on activity assays rather than a fictitious substrate-bound structure. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0052732 phosphoethanolamine phosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Human TNAP directly hydrolyzes phosphocholine and phosphoethanolamine. Reason: PMID:41145834 assays purified human TNAP residues 18–500 expressed in Expi293F cells (kinetics at pH 9.0), human serum from six donors and HuH-6 surface hydrolysis at pH 7.4. These experiments support the substrate chemistry. PC/PEA poses are docking predictions, while the experimental structures contain phosphate or inhibitor; the catalytic claim rests on activity assays rather than a fictitious substrate-bound structure. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0055062 phosphate ion homeostasis | IEA GO_REF:0000107 | ACCEPT | Summary: TNAP controls the local extracellular Pi/PPi balance at mineralizing surfaces. Reason: Mouse Alpl/Enpp1 double-knockout evidence in PMID:12082181 establishes opposing control of extracellular PPi and normalization with combined loss. Human TNAP directly generates Pi from PPi and nucleotides. Retain phosphate homeostasis at this local extracellular resolution; no renal transporter activity or independent systemic serum-phosphate set point is inferred. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0055074 calcium ion homeostasis | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: TNAP contributes to pathological extracellular calcium-phosphate deposition. Reason: PMID:28592560 studies ABCC6-mutant human skin fibroblasts under osteogenic conditions and Abcc6 mouse calcification. Increased TNAP activity and inhibition experiments support a role in this mineral-balance context. The broad calcium-homeostasis term does not require Ca transport by ALPL, but the pathological tissue setting is kept outside the compact physiological core. The retained broad annotation concerns participation in calcium/phosphate balance, not a claim that pathological calcification maintains a normal steady state. Unlike GO:0140928, it does not assert inhibition of mineral deposition; the direction-specific inhibitory assertion is contradicted by the positive TNAP-catalyzed removal of inhibitory PPi. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:28592560 A selective and orally bioavailable TNAP inhibitor prevented calcification in ABCC6 mutant cells in vitro and attenuated both the development and progression of calcification in Abcc6-/- mice in vivo |
| GO:0065010 extracellular membrane-bounded organelle | IEA GO_REF:0000120 | ACCEPT | Summary: Mineralizing matrix vesicles are a functional extracellular membrane-bounded compartment for TNAP. Reason: PMID:19874193 isolates mouse osteoblast matrix vesicles and compares nucleotide/PPi hydrolysis by genotype. TNAP-dependent Pi production and PPi removal supply direct compartmental function, consistent with the human ectophosphatase and skeletal evidence. The broad vesicle term is appropriate; it does not equate all matrix vesicles with endosome-derived urinary exosomes. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0071529 cementum mineralization | IEA GO_REF:0000107 | ACCEPT | Summary: TNAP phosphate chemistry supports dental cementum mineralization. Reason: This is the dental application of the mineralization mechanism rather than an unrelated developmental effect. The rat donor trace resolves to the cementum study PMID:17043865, and human hypophosphatasia independently has a well-established dental mineralization phenotype. Retain the curated transfer without claiming a newly read human cementoblast assay or using expression alone as the entire mechanism. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P08289 SUPPORTS TRANSFER Rat Alpl donor. MGI comparative Alpl graph resolves the cited response/mineralization provenance where stated; human transfer does not imply a new direct human assay. Supporting Evidence: PMID:9781036 Hypophosphatasia is an inherited disorder characterised by defective bone mineralisation and deficiency of serum and tissue liver/bone/kidney alkaline phosphatase (L/B/K ALP) activity. PMID:17043865 At this point, cementoblasts had shown intense TNSALP reaction and GBHA reactive particles (=calcium-GBHA complex) appeared on the root surface. |
| GO:0120162 positive regulation of cold-induced thermogenesis | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Mouse thermogenic-adipocyte TNAP performs the phosphocreatine-hydrolysis step of the futile creatine cycle. Reason: PMID:33981039 combines phosphocreatine hydrolysis, adipocyte perturbation, mitochondrial respiration and mouse energy-balance measurements. ALPL performs the hydrolytic step rather than merely being required for heat production. Retain the tissue-specific ortholog-supported process outside the compact human physiological core; direct recombinant human PCr chemistry is established, but direct human adipocyte localization and thermogenic flux were not resolved by the sources read. PMID:42020733 is current corroborating abstract-level evidence for glycerol regulation, not a substitute for unread Methods. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0140651 futile creatine cycle | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Mouse thermogenic-adipocyte TNAP performs the phosphocreatine-hydrolysis step of the futile creatine cycle. Reason: PMID:33981039 combines phosphocreatine hydrolysis, adipocyte perturbation, mitochondrial respiration and mouse energy-balance measurements. ALPL performs the hydrolytic step rather than merely being required for heat production. Retain the tissue-specific ortholog-supported process outside the compact human physiological core; direct recombinant human PCr chemistry is established, but direct human adipocyte localization and thermogenic flux were not resolved by the sources read. PMID:42020733 is current corroborating abstract-level evidence for glycerol regulation, not a substitute for unread Methods. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0140928 inhibition of non-skeletal tissue mineralization | IEA GO_REF:0000107 | REMOVE | Summary: The traced experiments support promotion, rather than inhibition, of non-skeletal mineralization by TNAP. Reason: Live GO:0140928 describes preventing calcium-phosphate deposition outside the skeleton. The MGI donor trace points to PMID:21490328, whose accessible abstract reports increased aortic calcification after TNAP overexpression; the available Discussion distinguishes PPi-generating/inhibitory NPP1/ANK from PPi-hydrolyzing TNAP. Independent full PMID:28592560 supports a pro-calcification role in ABCC6-mutant human fibroblasts and mice. This source-specific directional contradiction supports removal; it is not a claim that inhibitor experiments alone universally settle sign or that ALPL can never have an indirect protective effect. Propagation Review Root cause: SOURCE BAD Failure modes: REGULATORY SIGN INVERSION Sources checked: UniProtKB:P09242 SOURCE BAD Mouse Alpl GO:0140928 traces to PMID:21490328; the inspected overexpression result increases aortic calcification, opposite to inhibition. Exact source direction, not donor count, is challenged. Supporting Evidence: PMID:21490328 Overexpression of TNAP increased calcification of cultured aortas PMID:28592560 A selective and orally bioavailable TNAP inhibitor prevented calcification in ABCC6 mutant cells in vitro and attenuated both the development and progression of calcification in Abcc6-/- mice in vivo |
| GO:1904383 response to sodium phosphate | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Alpl expression/activity is measured in phosphate-driven mouse vascular-cell calcification. Reason: The MGI donor trace resolves to PMID:23523568. Methods distinguish beta-glycerophosphate/ascorbate from 3 mM sodium-phosphate culture conditions in primary mouse VSMCs. ALP activity accompanies calcification; FGF-23 protection does not change Alpl transcript in the reported comparison. Retain the curated contextual sodium-phosphate response without attributing FGF-23 signaling or protection to ALPL, or generalizing the assay to human tissue. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0006580 ethanolamine metabolic process | ISS GO_REF:0000024 | ACCEPT | Summary: TNAP directly releases ethanolamine and choline from their phosphorylated precursors. Reason: The inherited mouse metabolic-process assertions are corroborated by recombinant human TNAP kinetics, human serum and HuH-6 cell-surface hydrolysis in PMID:41145834, and human fibroblast PEA hydrolysis in PMID:2220817. ALPL performs a chemical step in these processes. Mouse liver/plasma lipid phenotypes and human-cell growth rescue support physiological context, but do not establish a direct TNAP lipid-transport activity or a measured human VLDL secretion flux. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0019695 choline metabolic process | ISS GO_REF:0000024 | ACCEPT | Summary: TNAP directly releases ethanolamine and choline from their phosphorylated precursors. Reason: The inherited mouse metabolic-process assertions are corroborated by recombinant human TNAP kinetics, human serum and HuH-6 cell-surface hydrolysis in PMID:41145834, and human fibroblast PEA hydrolysis in PMID:2220817. ALPL performs a chemical step in these processes. Mouse liver/plasma lipid phenotypes and human-cell growth rescue support physiological context, but do not establish a direct TNAP lipid-transport activity or a measured human VLDL secretion flux. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0052731 phosphocholine phosphatase activity | IDA PMID:41145834 TNAP dephosphorylates phosphocholine and phosphoethanolamine... | ACCEPT | Summary: Human TNAP directly hydrolyzes phosphocholine and phosphoethanolamine. Reason: PMID:41145834 assays purified human TNAP residues 18–500 expressed in Expi293F cells (kinetics at pH 9.0), human serum from six donors and HuH-6 surface hydrolysis at pH 7.4. These experiments support the substrate chemistry. PC/PEA poses are docking predictions, while the experimental structures contain phosphate or inhibitor; the catalytic claim rests on activity assays rather than a fictitious substrate-bound structure. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0052732 phosphoethanolamine phosphatase activity | IDA PMID:41145834 TNAP dephosphorylates phosphocholine and phosphoethanolamine... | ACCEPT | Summary: Human TNAP directly hydrolyzes phosphocholine and phosphoethanolamine. Reason: PMID:41145834 assays purified human TNAP residues 18–500 expressed in Expi293F cells (kinetics at pH 9.0), human serum from six donors and HuH-6 surface hydrolysis at pH 7.4. These experiments support the substrate chemistry. PC/PEA poses are docking predictions, while the experimental structures contain phosphate or inhibitor; the catalytic claim rests on activity assays rather than a fictitious substrate-bound structure. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0004427 inorganic diphosphate phosphatase activity | EXP PMID:12162492 Kinetic characterization of hypophosphatasia mutations with ... | ACCEPT | Summary: TNAP hydrolyzes inorganic diphosphate to phosphate. Reason: The RHEA:24576 chemistry agrees with assays of purified human TNAP and hypophosphatasia variants at physiological pH. Removing extracellular PPi promotes hydroxyapatite propagation; this is a principal mineralization mechanism, alongside nucleotide-derived Pi supply. Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0005758 mitochondrial intermembrane space | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Mouse thermogenic adipocytes provide positive mitochondrial-localization evidence. Reason: PMID:33981039 directly localizes endogenous and tagged mouse TNAP to thermogenic-adipocyte mitochondria, using knockout-controlled imaging, fractionation, protease protection and APEX2. The construct is mouse P09242 and the tissue experiments are murine. Retain the conserved, tissue-restricted localization as non-core here; direct human recombinant phosphocreatine hydrolysis in the same paper does not by itself establish human mitochondrial targeting. This is a model boundary, not evidence of contamination or impossibility for a GPI-anchored protein. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0005886 plasma membrane | EXP PMID:23688511 An asparagine at position 417 of tissue-nonspecific alkaline... | ACCEPT | Summary: Human TNAP variants and wild type are assayed for cell-surface delivery. Reason: PMID:23688511 and PMID:25982064 express human TNAP in COS-1/CHO-K1 hosts and distinguish surface trafficking from dimer assembly and catalytic activity. A heterologous host does not make the expressed human construct a nonhuman protein. The positive surface-localization evidence supports the broad plasma-membrane assertion. Supporting Evidence: PMID:23688511 this mutant failed to assemble into a dimer structure, which is needed for the catalytic function of TNSALP, as evidenced by newly developed SDS-PAGE as well as sucrose-density-gradient centrifugation. PMID:25982064 TNSALP (WT) largely formed a functional dimeric structure, while TNSALP (P108L) was found to be present as a monomer in the cell. |
| GO:0005886 plasma membrane | EXP PMID:25982064 Molecular phenotype of tissue-nonspecific alkaline phosphata... | ACCEPT | Summary: Human TNAP variants and wild type are assayed for cell-surface delivery. Reason: PMID:23688511 and PMID:25982064 express human TNAP in COS-1/CHO-K1 hosts and distinguish surface trafficking from dimer assembly and catalytic activity. A heterologous host does not make the expressed human construct a nonhuman protein. The positive surface-localization evidence supports the broad plasma-membrane assertion. Supporting Evidence: PMID:23688511 this mutant failed to assemble into a dimer structure, which is needed for the catalytic function of TNSALP, as evidenced by newly developed SDS-PAGE as well as sucrose-density-gradient centrifugation. PMID:25982064 TNSALP (WT) largely formed a functional dimeric structure, while TNSALP (P108L) was found to be present as a monomer in the cell. |
| GO:0016887 ATP hydrolysis activity | ISS GO_REF:0000024 | MODIFY | Summary: Human TNAP directly hydrolyzes ATP, but the present GO ATP-hydrolysis term carries an energy-coupling convention. Reason: PMID:19874193 measures ATP-to-ADP/Pi hydrolysis by soluble human TNAP at pH 7.4, alongside mouse matrix-vesicle experiments. Live GO:0016887 has a comment restricting usage to ATP-powered reactions and a part_of relation to ATP-dependent activity. No mechanical or chemical coupling of ATP energy is shown here. Refine to the immediate reaction parent GO:0017111, whose definition includes hydrolysis of a ribonucleoside triphosphate without that restriction. ATP is the measured substrate; this does not assert that every NTP is hydrolyzed. Preserve the positive chemistry and original source rather than reclassifying it as weak incidental activity. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Proposed replacements: ribonucleoside triphosphate phosphatase activity Supporting Evidence: PMID:19874193 A soluble epitope tagged from of human TNAP was produced and purified as described previously. PMID:19874193 ATPase, pyrophosphatase (PPiase), ADPase, and AMPase activities were assayed discontinuously by measuring the amount of inorganic phosphate liberated |
| GO:0031966 mitochondrial membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Mouse thermogenic adipocytes provide positive mitochondrial-localization evidence. Reason: PMID:33981039 directly localizes endogenous and tagged mouse TNAP to thermogenic-adipocyte mitochondria, using knockout-controlled imaging, fractionation, protease protection and APEX2. The construct is mouse P09242 and the tissue experiments are murine. Retain the conserved, tissue-restricted localization as non-core here; direct human recombinant phosphocreatine hydrolysis in the same paper does not by itself establish human mitochondrial targeting. This is a model boundary, not evidence of contamination or impossibility for a GPI-anchored protein. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0043262 ADP phosphatase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Human TNAP catalyzes ADP dephosphorylation as part of local Pi generation. Reason: RHEA:61436 and GO:0043262 specify ADP-to-AMP/Pi hydrolysis, without an energy-coupling requirement. PMID:19874193 directly assays recombinant human TNAP with ADP at pH 7.4 and separately analyzes nucleotide turnover in mouse matrix vesicles. This is a supported catalytic component of the mineralization-associated substrate repertoire. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:19874193 A soluble epitope tagged from of human TNAP was produced and purified as described previously. PMID:19874193 ATPase, pyrophosphatase (PPiase), ADPase, and AMPase activities were assayed discontinuously by measuring the amount of inorganic phosphate liberated |
| GO:0050187 phosphoamidase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Phosphocreatine hydrolysis is directly measured for recombinant human TNAP. Reason: PMID:33981039 explicitly assays commercial recombinant human TNAP with phosphocreatine at 37 degrees C and pH 7.8, deriving substrate kinetics. GO:0050187 has exactly the phosphocreatine-to-creatine/Pi reaction (RHEA:12977), despite the broad-sounding phosphoamidase label. Thus the human chemistry is not supported only by mouse similarity. Mouse adipocyte localization and thermogenic physiology remain separately scoped. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:33981039 recombinant human TNAP hydrolyzes PCr robustly (Extended Data Fig. 1e–g). |
| GO:0004035 alkaline phosphatase activity | IDA PMID:12162492 Kinetic characterization of hypophosphatasia mutations with ... | ACCEPT | Summary: Alkaline phosphatase activity is directly measured for human TNAP. Reason: Recombinant human TNAP hydrolyzes pNPP and physiological phosphoester substrates. The general alkaline phosphatase term captures a broad substrate repertoire rather than a single exclusive reaction; the more specific substrate rows add complementary coverage. Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0004035 alkaline phosphatase activity | IDA PMID:33821301 Novel mutation in the ALPL gene with a dominant negative eff... | ACCEPT | Summary: The human G82R TNAP variant lacks alkaline-phosphatase activity and suppresses wild-type activity in coexpression assays. Reason: The PMID:33821301 abstract explicitly reports transfected COS-7 assays of a human ALPL variant and dominant-negative activity. This supports the alkaline-phosphatase function; it does not establish that all hypophosphatasia variants act through one dimerization defect. |
| GO:0005509 calcium ion binding | IDA PMID:11395499 Structural evidence for a functional role of human tissue no... | ACCEPT | Summary: Human TNAP binds a structural calcium ion. Reason: PMID:11395499 combines TNAP homology modeling with the placental-AP structure and X-ray fluorescence; its complete original experimental allocation was not recovered. Retain the curated human IDA with independent direct corroboration from the human TNAP structure in PMID:41145834 and deposited 9SH5. A structural metal site is part of the functional enzyme and need not itself catalyze bond cleavage to count as core binding. Supporting Evidence: PMID:41145834 The same divalent cations were identified, including the three essential cations in the catalytic site (two zinc ions and one magnesium ion), along with a calcium ion at the CA cluster |
| GO:0005886 plasma membrane | IDA PMID:2220817 Alkaline phosphatase (tissue-nonspecific isoenzyme) is a pho... | MODIFY | Summary: Human fibroblast experiments specifically place active TNAP on the external plasma-membrane face. Reason: PMID:2220817 tests membrane-impermeable substrates, extracellular acid inactivation and PI-PLC release in intact human fibroblasts. These assays resolve the external side more precisely than plasma membrane. Refine this directly supported row to GO:0009897 and withdraw the redundant prior authored NEW for the same location; other broad source rows remain valid. Proposed replacements: external side of plasma membrane Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0005886 plasma membrane | IDA PMID:33821301 Novel mutation in the ALPL gene with a dominant negative eff... | ACCEPT | Summary: Plasma-membrane localization is independently established for human TNAP. Reason: The available PMID:33821301 abstract centers on catalytic loss and dominant-negative G82R and does not expose the original localization experiment. Defer to its curated IDA for this clearly correct broad location, corroborated by independent human fibroblast ectoenzyme assays. Do not claim that the abstract itself measures surface targeting. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0016462 pyrophosphatase activity | IDA PMID:12162492 Kinetic characterization of hypophosphatasia mutations with ... | MODIFY | Summary: The broad acid-anhydride hydrolase annotation can be made substrate-specific. Reason: The inherited mineralization assertion and PMID:12162492 substrate experiments specifically support inorganic PPi hydrolysis. Refine to GO:0004427. This refinement does not deny ATP/ADP hydrolysis established independently; GO:0016462 is a broad parent that includes several anhydride substrates. Proposed replacements: inorganic diphosphate phosphatase activity Supporting Evidence: PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0030282 bone mineralization | ISS GO_REF:0000024 | ACCEPT | Summary: Conserved TNAP phosphatase chemistry supports bone mineralization. Reason: Mouse Alpl genetic/biochemical studies and direct human TNAP enzymology agree with human hypophosphatasia. TNAP consumes the mineralization inhibitor PPi and supplies Pi from extracellular substrates; the product therefore performs part of the mineralization process rather than serving only as a disease marker. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. Supporting Evidence: PMID:9781036 Hypophosphatasia is an inherited disorder characterised by defective bone mineralisation and deficiency of serum and tissue liver/bone/kidney alkaline phosphatase (L/B/K ALP) activity. PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0033883 pyridoxal phosphatase activity | IDA PMID:12162492 Kinetic characterization of hypophosphatasia mutations with ... | ACCEPT | Summary: TNAP dephosphorylates extracellular pyridoxal phosphate. Reason: Human fibroblast ectoenzyme experiments and purified recombinant human TNAP substrate-selectivity measurements establish this catalytic step. It converts extracellular PLP to membrane-permeant pyridoxal, supporting vitamin B6 availability. Distinct mutant substrate effects are measured, but those biochemical differences alone do not assign a clinical seizure phenotype to each variant. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0033883 pyridoxal phosphatase activity | IDA PMID:2220817 Alkaline phosphatase (tissue-nonspecific isoenzyme) is a pho... | ACCEPT | Summary: TNAP dephosphorylates extracellular pyridoxal phosphate. Reason: Human fibroblast ectoenzyme experiments and purified recombinant human TNAP substrate-selectivity measurements establish this catalytic step. It converts extracellular PLP to membrane-permeant pyridoxal, supporting vitamin B6 availability. Distinct mutant substrate effects are measured, but those biochemical differences alone do not assign a clinical seizure phenotype to each variant. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0052732 phosphoethanolamine phosphatase activity | IDA PMID:2220817 Alkaline phosphatase (tissue-nonspecific isoenzyme) is a pho... | ACCEPT | Summary: Intact human fibroblasts dephosphorylate extracellular phosphoethanolamine through TNAP. Reason: PMID:2220817 compares normal and hypophosphatasia fibroblasts and resolves the outward-facing lipid-anchored PEA/PLP phosphatase. This is direct substrate chemistry and is independently reinforced by purified human TNAP in PMID:41145834. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0120162 positive regulation of cold-induced thermogenesis | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Mouse thermogenic-adipocyte TNAP performs the phosphocreatine-hydrolysis step of the futile creatine cycle. Reason: PMID:33981039 combines phosphocreatine hydrolysis, adipocyte perturbation, mitochondrial respiration and mouse energy-balance measurements. ALPL performs the hydrolytic step rather than merely being required for heat production. Retain the tissue-specific ortholog-supported process outside the compact human physiological core; direct recombinant human PCr chemistry is established, but direct human adipocyte localization and thermogenic flux were not resolved by the sources read. PMID:42020733 is current corroborating abstract-level evidence for glycerol regulation, not a substitute for unread Methods. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0055074 calcium ion homeostasis | IDA PMID:28592560 Ectopic calcification in pseudoxanthoma elasticum responds t... | KEEP AS NON CORE | Summary: TNAP contributes to pathological extracellular calcium-phosphate deposition. Reason: PMID:28592560 studies ABCC6-mutant human skin fibroblasts under osteogenic conditions and Abcc6 mouse calcification. Increased TNAP activity and inhibition experiments support a role in this mineral-balance context. The broad calcium-homeostasis term does not require Ca transport by ALPL, but the pathological tissue setting is kept outside the compact physiological core. The retained broad annotation concerns participation in calcium/phosphate balance, not a claim that pathological calcification maintains a normal steady state. Unlike GO:0140928, it does not assert inhibition of mineral deposition; the direction-specific inhibitory assertion is contradicted by the positive TNAP-catalyzed removal of inhibitory PPi. Supporting Evidence: PMID:28592560 A selective and orally bioavailable TNAP inhibitor prevented calcification in ABCC6 mutant cells in vitro and attenuated both the development and progression of calcification in Abcc6-/- mice in vivo |
| GO:0005758 mitochondrial intermembrane space | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Mouse thermogenic adipocytes provide positive mitochondrial-localization evidence. Reason: PMID:33981039 directly localizes endogenous and tagged mouse TNAP to thermogenic-adipocyte mitochondria, using knockout-controlled imaging, fractionation, protease protection and APEX2. The construct is mouse P09242 and the tissue experiments are murine. Retain the conserved, tissue-restricted localization as non-core here; direct human recombinant phosphocreatine hydrolysis in the same paper does not by itself establish human mitochondrial targeting. This is a model boundary, not evidence of contamination or impossibility for a GPI-anchored protein. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0031966 mitochondrial membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Mouse thermogenic adipocytes provide positive mitochondrial-localization evidence. Reason: PMID:33981039 directly localizes endogenous and tagged mouse TNAP to thermogenic-adipocyte mitochondria, using knockout-controlled imaging, fractionation, protease protection and APEX2. The construct is mouse P09242 and the tissue experiments are murine. Retain the conserved, tissue-restricted localization as non-core here; direct human recombinant phosphocreatine hydrolysis in the same paper does not by itself establish human mitochondrial targeting. This is a model boundary, not evidence of contamination or impossibility for a GPI-anchored protein. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:P09242 SUPPORTS TRANSFER Mouse Alpl donor. Term-specific primary source and human corroboration/model boundary are assessed in the reason; mouse tissue assays are not relabeled as human experiments. |
| GO:0001649 osteoblast differentiation | HDA PMID:16210410 Differential expression profiling of membrane proteins by qu... | MARK AS OVER ANNOTATED | Summary: The human membrane survey measures TNAP as a differentiation-associated enzyme rather than demonstrating its performance of a differentiation step. Reason: The original full PMID:16210410 was recovered from an author upload after publisher routes failed. Its Methods/Results use calcitriol-treated hMSC-TERT cells at day 4: membrane-proteome ALPL increases more than 27-fold and catalytic histochemical staining confirms induction. The inspected main study contains no ALPL perturbation or assay assigning it a step in acquisition of osteoblast identity, the process defined by GO:0001649. This is positive expression/activity evidence during early lineage commitment, not evidence that ALPL cannot affect differentiation in another setting. Mark this source-specific process inference as over-annotated while preserving the measured induction and independently established mineralization chemistry. |
| GO:0016020 membrane | HDA PMID:16210410 Differential expression profiling of membrane proteins by qu... | ACCEPT | Summary: The human membrane-proteome survey supports the broad membrane location. Reason: The externally recovered full PMID:16210410 identifies ALPL in a postnuclear/postmitochondrial membrane preparation from human hMSC-TERT cells, with 9% sequence coverage. Retain this survey-resolution HDA; it is not a purified plasma-membrane fraction. Independent human TNAP topology corroborates membrane association, but refining this survey itself to a precisely assayed leaflet would overstate its resolution. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0005576 extracellular region | TAS Reactome:R-HSA-8940388 | ACCEPT | Summary: Extracellular TNAP includes an enzymatically active soluble pool. Reason: GPI-anchor release and circulating TNAP are compatible with this broad compartment. PMID:41145834 measures TNAP-sensitive phosphocholine and phosphoethanolamine hydrolysis in serum from six human donors at physiological pH, giving functional evidence beyond passive release. The Reactome source describes GPLD1 acting on a GPI-anchored protein; it does not make ALPL the GPI-cleaving enzyme, and its generic cached summary alone does not resolve an ALPL-specific entity. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0005886 plasma membrane | TAS Reactome:R-HSA-8940388 | ACCEPT | Summary: The Reactome GPI-anchor substrate context is consistent with membrane-associated TNAP. Reason: R-HSA-8940388 describes GPLD1 hydrolyzing GPI anchors; its generic cached summary does not itself identify every substrate. Retain the curated plasma-membrane assertion using independent human TNAP PI-PLC/ectophosphatase evidence. ALPL is the anchored substrate in this context, not the phospholipase catalyst. Supporting Evidence: PMID:2220817 TNS-ALP acts physiologically as a lipid-anchored PEA and PLP ectophosphatase |
| GO:0070062 extracellular exosome | HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... | UNDECIDED | Summary: A prostate-secretion exosome proteome is the source of this ALPL localization assertion. Reason: The actual cached PMID:23533145 body describes human expressed-prostatic-secretion urine exosome proteomics, but the ALPL-specific supplementary identification row was not recovered. Retain source-specific uncertainty rather than asserting contamination or an incorrect gene from a broad survey. The independent urinary-exosome ALPL identification in PMID:19056867 Table 1 supports this location in another sample context, but does not verify the unrecovered ALPL row in this prostate-secretion dataset. This source-specific uncertainty does not negate the independently retained exosome annotation or established matrix-vesicle activity. |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | KEEP AS NON CORE | Summary: ALPL is detected in a human urinary exosome-enriched membrane fraction. Reason: Externally indexed full PMID:19056867/PMC2637050 Table 1 explicitly lists ALPL tissue-nonspecific alkaline-phosphatase precursor with three unique peptides and four identifications. This resolves the target hit despite the abstract-only local cache. Preserve the positive contextual localization; the study does not establish TNAP catalysis or exosome biogenesis in that fraction. |
| GO:0016462 pyrophosphatase activity | IDA PMID:19874193 Kinetic analysis of substrate utilization by native and TNAP... | MODIFY | Summary: Human TNAP hydrolyzes defined inorganic and nucleotide phosphoanhydrides. Reason: PMID:19874193 directly assays soluble human TNAP with PPi, ATP and ADP at pH 7.4, separately from mouse matrix-vesicle genetics. Replace the generic pyrophosphatase parent with the measured inorganic diphosphate phosphatase activity for the mineralization unit; ATP/ADP chemistry remains explicitly covered in the other rows and this reason. The paper is not restricted to inorganic PPi. Proposed replacements: inorganic diphosphate phosphatase activity Supporting Evidence: PMID:19874193 A soluble epitope tagged from of human TNAP was produced and purified as described previously. PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0033280 response to vitamin D | IEP PMID:17023519 Evidence for auto/paracrine actions of vitamin D in bone: 1a... | KEEP AS NON CORE | Summary: Human osteoblast alkaline-phosphatase activity changes with vitamin D treatment. Reason: PMID:17023519 examines vitamin-D metabolism in human bone-derived cells and measures ALP activity alongside differentiation/mineralization readouts. Retain the expression/activity response at the IEP level; CYP27B1, rather than ALPL, performs vitamin-D hydroxylation. No receptor or hormone-metabolism activity is assigned to TNAP. |
| GO:0001501 skeletal system development | TAS PMID:9781036 Identification of fifteen novel mutations in the tissue-nons... | ACCEPT | Summary: TNAP-dependent mineralization contributes to skeletal development. Reason: GO:0001501 covers development of the skeleton to its mature structure, not only embryonic pattern specification. Human hypophosphatasia in PMID:9781036 and established TNAP substrate chemistry support that broad process. Retain this correct TAS resolution; the compact core can name bone mineralization without requiring a second redundant broad core entry. Supporting Evidence: PMID:9781036 Hypophosphatasia is an inherited disorder characterised by defective bone mineralisation and deficiency of serum and tissue liver/bone/kidney alkaline phosphatase (L/B/K ALP) activity. PMID:12162492 We also determined the ability of the mutants to metabolize two natural substrates of TNAP, that is, pyridoxal-5'-phosphate (PLP) and inorganic pyrophosphate (PPi), at physiological pH. |
| GO:0008270 zinc ion binding | IDA PMID:41145834 TNAP dephosphorylates phosphocholine and phosphoethanolamine... | NEW | Summary: Direct human TNAP structures identify its catalytic zinc and magnesium cofactors. Reason: The human protein itself coordinates these ions. PMID:41145834 reports two zinc ions and one magnesium ion in the catalytic site; live 9SH5 identifies human P05186 with deposited Zn/Mg ligands and the same article title/authors. These binding terms are neither ancestors nor descendants of the existing calcium-binding or catalytic terms. Their parents are metal/transition-metal binding, and no matching P05186 GO-CAM activity was found locally. ALPI/ALPP carry seeded metal-binding assertions, a comparator consistent with the chemistry but not the primary reason for adding it. Retain the prior NEW based on direct human structure, not a proposed missing family function. Supporting Evidence: PMID:41145834 The same divalent cations were identified, including the three essential cations in the catalytic site (two zinc ions and one magnesium ion), along with a calcium ion at the CA cluster |
| GO:0000287 magnesium ion binding | IDA PMID:41145834 TNAP dephosphorylates phosphocholine and phosphoethanolamine... | NEW | Summary: Direct human TNAP structures identify its catalytic zinc and magnesium cofactors. Reason: The human protein itself coordinates these ions. PMID:41145834 reports two zinc ions and one magnesium ion in the catalytic site; live 9SH5 identifies human P05186 with deposited Zn/Mg ligands and the same article title/authors. These binding terms are neither ancestors nor descendants of the existing calcium-binding or catalytic terms. Their parents are metal/transition-metal binding, and no matching P05186 GO-CAM activity was found locally. ALPI/ALPP carry seeded metal-binding assertions, a comparator consistent with the chemistry but not the primary reason for adding it. Retain the prior NEW based on direct human structure, not a proposed missing family function. Supporting Evidence: PMID:41145834 The same divalent cations were identified, including the three essential cations in the catalytic site (two zinc ions and one magnesium ion), along with a calcium ion at the CA cluster |
| GO:0042803 protein homodimerization activity | IDA PMID:23688511 An asparagine at position 417 of tissue-nonspecific alkaline... | NEW | Summary: Human TNAP homodimer assembly is directly measured and functionally coupled to enzyme activity. Reason: PMID:23688511 compares WT human TNAP with surface-delivered N417S using SDS-PAGE and sucrose-gradient assembly assays; PMID:25982064 similarly distinguishes WT dimer from P108L monomer. Human 9SH5 independently provides a dimeric structural assembly with gel-filtration support. GO:0042803 names binding an identical protein to form a dimer; none of its binding/dimerization ancestors is seeded for ALPL, and no local P05186 GO-CAM was found. Retain this prior direct-evidence NEW without asserting that all dominant-negative alleles share this mechanism or that the two earlier studies are independent laboratories. Supporting Evidence: PMID:23688511 this mutant failed to assemble into a dimer structure, which is needed for the catalytic function of TNSALP, as evidenced by newly developed SDS-PAGE as well as sucrose-density-gradient centrifugation. PMID:25982064 TNSALP (WT) largely formed a functional dimeric structure, while TNSALP (P108L) was found to be present as a monomer in the cell. |
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Download this section (compressed HTML)Q: How broadly does endogenous human TNAP localize to the intermembrane space of thermogenic adipocytes? Human recombinant phosphocreatine hydrolysis is established, whereas the detailed mitochondrial targeting and thermogenic-flux experiments read here are mouse studies.
Q: Should extracellular ATP-to-ADP/Pi phosphatases use GO:0017111, given the energy-coupling comment and ATP-dependent-activity parent relationship of GO:0016887 despite its reaction-based definition?
Q: Does ALPL perform a separable step in osteoblast fate acquisition beyond its established mineralization chemistry? The recovered full PMID:16210410 measures induction during early lineage commitment, rather than demonstrating that step.
Q: Can the ALPL peptide-level identification and purification context in the PMID:23533145 exosome supplement be recovered to resolve its source-specific localization assertion?
Q: How do substrate concentration, pH, compartment and allosteric regulation set the relative in-vivo fluxes of TNAP toward PPi, nucleotides, PLP, phosphocholine, phosphoethanolamine and phosphocreatine? The 2026 glycerol-regulation report is relevant, but its complete Methods/Results were not recovered in this audit.
Q: Which positive process term best represents TNAP-promoted non-skeletal calcification? GO:0140928 has the opposite sign for the traced experiments; a new opposite-direction term is not claimed to be absent without a complete ontology search.
Experiment: Combine endogenous human ALPL tagging, knockout-controlled fractionation and protease protection with isotope-resolved phosphocreatine turnover and respiration. Distinguish mitochondrial targeting from the already established recombinant human enzyme reaction.
Hypothesis: Human thermogenic-adipocyte TNAP uses a mitochondrial phosphocreatine-hydrolysis mechanism analogous to the measured mouse pathway.
Type: localization and isotope-resolved metabolic flux
Experiment: Compare matched physiological-pH kinetics of human TNAP variants on PPi, ATP, ADP, AMP, PLP, phosphocholine, phosphoethanolamine and phosphocreatine, then test selected separable defects in human mineralizing and hepatocyte models. Measure uptake and lipoprotein secretion directly rather than inferring flux solely from growth or lipid accumulation.
Hypothesis: The relative contribution of TNAP substrates depends on tissue context and human disease allele.
Type: comparative enzymology and cell-based flux
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