Alpl encodes mouse tissue-nonspecific alkaline phosphatase (TNAP), the rodent orthologue of human ALPL and the organism in which most of what is believed about this enzyme was actually established. It is a homodimeric, GPI-anchored Zn/Zn/Mg metalloenzyme displayed on the outer leaflet of the plasma membrane and on osteoblast- and chondrocyte-derived matrix vesicles, hydrolysing phosphate monoesters at alkaline pH through a covalent phosphoseryl intermediate at Ser110. Its principal substrate is extracellular inorganic pyrophosphate, the endogenous inhibitor of hydroxyapatite propagation, and the Alpl-null mouse reproduces hypophosphatasia: defective skeletal and dental mineralization, with compound ablation alongside Phospho1 separating the initiation of crystal formation inside matrix vesicles from its propagation into the extracellular matrix. The enzyme also dephosphorylates pyridoxal 5'-phosphate, and knockout mice die of seizures from defective vitamin B6 metabolism, the clearest demonstration in any species that this reaction is physiologically essential. Two further roles were discovered in this organism. TNAP dephosphorylates phosphocholine and phosphoethanolamine, enabling hepatocyte choline uptake, and knockouts develop liver steatosis. And in thermogenic fat cells TNAP is localised to mitochondria, where it acts as the phosphocreatine phosphatase of the futile creatine cycle; adipocyte-specific ablation reduces energy expenditure and causes rapid-onset obesity.
Definition: A process in which a gene product increases the deposition of calcium phosphate mineral in tissue that is not normally mineralized, for example by degrading extracellular inorganic pyrophosphate or other endogenous inhibitors of hydroxyapatite propagation in vascular or soft tissue.
Justification: GO offers GO:0140928 for the inhibiting direction but nothing for the promoting one, which forces curators of pyrophosphate-degrading enzymes into a directionally incorrect annotation. Mouse Alpl is the clearest case and the origin of the problem: its GO:0140928 rows trace to an experiment in which TNAP overexpression increased aortic calcification. A term in the promoting direction would let this well-supported biology be recorded correctly rather than dropped or expressed as a NOT annotation. Enpp1 and Ank, the other arms of the same paper, would keep GO:0140928.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004035 alkaline phosphatase activity | IBA GO_REF:0000033 | ACCEPT | Summary: The core molecular function. Mouse Alpl is one of the seeds behind the family-wide PAINT node for this term, and the activity is directly measured in several of the cited studies. Reason: Correct and ancestral. The family review (PANTHER:PTHR11596) found the catalytic serine and the Zn/Zn/Mg ligands conserved in all twenty-seven reviewed members, with mouse Alpl carrying serine at position 110, so the term is safe here on residue grounds as well as experimental ones. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Plasma membrane. TNAP is GPI-anchored on the outer leaflet with its catalytic domain facing outward, so this is genuinely where the enzyme acts. Reason: Correct. The family review records the PAINT node for this term as scoped to Eumetazoa and seeded partly from this gene, which is the right boundary: the bacterial members are periplasmic and the fungal ones vacuolar. |
| GO:0030282 bone mineralization | IBA GO_REF:0000033 | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. |
| GO:0004035 alkaline phosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: The core molecular function. Mouse Alpl is one of the seeds behind the family-wide PAINT node for this term, and the activity is directly measured in several of the cited studies. Reason: Correct and ancestral. The family review (PANTHER:PTHR11596) found the catalytic serine and the Zn/Zn/Mg ligands conserved in all twenty-seven reviewed members, with mouse Alpl carrying serine at position 110, so the term is safe here on residue grounds as well as experimental ones. |
| GO:0004427 inorganic diphosphate phosphatase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Hydrolysis of inorganic pyrophosphate, measured directly in mouse matrix vesicles and in further studies of skeletal mineralization. This is the reaction that links Alpl to bone. Reason: Core. Removing extracellular PPi lifts the brake on hydroxyapatite propagation, and the mouse knockout phenotype is the strongest evidence anywhere that this reaction matters in vivo. More specific and more informative than the generic pyrophosphatase parent. Supporting Evidence: 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:0000044 | ACCEPT | Summary: Mitochondrial intermembrane space. Unlike in other cells, TNAP in thermogenic fat cells localises to mitochondria, which is where futile creatine cycling occurs. Reason: Topologically unusual for a GPI-anchored protein and therefore worth stating carefully, but this is the direct observation on which the human ISS and IEA rows depend. Accepting it here while keeping the human rows non-core is the correct asymmetry: the evidence is in this organism. Supporting Evidence: PMID:33981039 Unlike in other cells, TNAP in thermogenic fat cells is localized to the mitochondria, where futile creatine cycling occurs. file:mouse/Alpl/Alpl-deep-research-falcon.md Biochemical purification found Alpl/TNAP **sevenfold enriched** in the active mitochondrial phosphocreatine-phosphatase fraction. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Plasma membrane. TNAP is GPI-anchored on the outer leaflet with its catalytic domain facing outward, so this is genuinely where the enzyme acts. Reason: Correct. The family review records the PAINT node for this term as scoped to Eumetazoa and seeded partly from this gene, which is the right boundary: the bacterial members are periplasmic and the fungal ones vacuolar. |
| GO:0008253 5'-nucleotidase activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: 5'-nucleotidase activity, the AMP-to-adenosine step completing the stepwise ectonucleotidase cascade. Reason: A real catalytic capability, but in most tissues this step is dominated by the dedicated ecto-5'-nucleotidase NT5E, so the quantitative contribution of TNAP is context-dependent. |
| GO:0016791 phosphatase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping to the generic parent term, discarding the alkaline pH optimum that the source signature itself names. Reason: The InterPro entries behind this row are the alkaline phosphatase domain and its active site, which license GO:0004035, a descendant that is directly supported here many times over. Applied consistently across all six alkaline phosphatase reviews in this set. Proposed replacements: alkaline phosphatase activity |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: ATP hydrolysis activity. The enzyme does hydrolyse ATP, and in osteoblast-derived matrix vesicles ATP was the main substrate hydrolysed, with TNAP the responsible enzyme. Reason: The chemistry is real but the term carries an unhelpful connotation: it normally labels ATPases that couple hydrolysis to work, whereas TNAP strips the terminal phosphate as a promiscuous phosphomonoesterase with no energy coupling. Retained as non-core to record the ectonucleotidase capability without implying it is an ATPase. Supporting Evidence: PMID:19874193 The lack of TNAP had the most pronounced effect on the hydrolysis of all physiologic substrates. |
| GO:0031966 mitochondrial membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Mitochondrial membrane, the companion localisation from the same study, with TNAP described as tethered to mitochondrial membranes in thermogenic adipocytes. Reason: Same basis and same assessment as the intermembrane space row: direct evidence in this organism, restricted to one cell type but not therefore doubtful. |
| GO:0043262 ADP phosphatase activity | IEA GO_REF:0000116 | KEEP AS NON CORE | Summary: ADP phosphatase activity, the middle step of stepwise extracellular ATP degradation, measured in matrix vesicles. Reason: Genuine but ancillary: purinergic nucleotide turnover is shared with the ENPP, CD39 and CD73 systems and is not the reaction whose loss produces the knockout phenotype. |
| GO:0050187 phosphoamidase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Phosphoamidase activity, defined narrowly as hydrolysis of N-phosphocreatine to creatine and phosphate. In mouse this is directly demonstrated: thermogenic fat cells have robust phosphocreatine phosphatase activity attributable to TNAP. Reason: Accepted here on direct evidence, in contrast to the human record where the same term rests only on similarity to this gene. This is the annotation that grounds the whole futile creatine cycle story, and the mouse is where it was established. Supporting Evidence: PMID:33981039 Thermogenic fat cells have robust phosphocreatine phosphatase activity, which is attributed to tissue-nonspecific alkaline phosphatase (TNAP). |
| GO:0005509 calcium ion binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Calcium ion binding, corresponding to the mammalian-specific structural calcium site that has no counterpart in the bacterial enzyme. Reason: Real and structurally located: the family review confirms the four calcium ligands are present as an invariant Glu-Phe-Glu-Asp set in all eight animal members examined and absent from all three microbial ones. Non-core because the site is structural rather than catalytic and does not influence phosphatase activity. |
| GO:0005576 extracellular region | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Extracellular region, reached when the GPI anchor is cleaved and catalytically active enzyme is released into extracellular fluid and serum. Reason: True but unspecific, and downstream of where the enzyme does its defining work. Worth keeping because circulating alkaline phosphatase is the standard clinical readout, but it is a released form rather than a functional compartment. |
| GO:0016462 pyrophosphatase activity | IEA GO_REF:0000107 | MODIFY | Summary: The broad parent term covering hydrolysis of any pyrophosphate bond, which also spans nucleoside triphosphatases. The experiments behind these rows measured hydrolysis of inorganic pyrophosphate specifically. Reason: GO:0004427 is a descendant of this term and is already annotated to mouse Alpl from the same experiments. Using the parent understates what was measured and blurs the distinction between destroying inorganic PPi, which is what governs mineralization, and hydrolysing a nucleotide anhydride bond. The same modification is applied in the human ALPL review. Proposed replacements: inorganic diphosphate phosphatase activity |
| GO:0032496 response to lipopolysaccharide | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Response to lipopolysaccharide. TNAP can dephosphorylate the lipid A moiety of LPS, though in the gut that role belongs mainly to the intestinal isozyme. Reason: Plausible and consistent with the enzyme's broad substrate tolerance, but peripheral here. Note that a response-to term describes the cell's reaction to a stimulus, which is a weaker and different claim than dephosphorylating LPS, and should not be read as supporting the catalytic claim. |
| GO:0032868 response to insulin | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Response to insulin, an expression-response annotation transferred by orthology. Reason: Regulation of the gene rather than a function of the protein, and not demonstrated in this organism. Retained because there is no positive evidence against it. |
| GO:0033280 response to vitamin D | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Response to vitamin D, transferred by orthology from the human osteoblast studies in which 1,25-dihydroxyvitamin D3 induces alkaline phosphatase activity. Reason: A real and well-documented regulatory relationship, but it records that Alpl is a vitamin D-responsive gene rather than anything about the enzyme's activity. |
| GO:0033883 pyridoxal phosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Pyridoxal 5'-phosphate phosphatase activity. In mouse this is not an incidental substrate preference: Alpl-null mice die of seizures caused by defective vitamin B6 metabolism, which is the cleanest in vivo demonstration of the reaction's importance in the whole family. Reason: Core, and the mouse is where the causal evidence lives. Because PLP cannot cross the plasma membrane, extracellular dephosphorylation by TNAP is the obligatory step supplying cells with usable vitamin B6. |
| GO:0036005 response to macrophage colony-stimulating factor | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Response to macrophage colony-stimulating factor, an orthology- transferred stimulus-response annotation from a bone-cell culture context. Reason: Weakly informative and at the far periphery of what is known about this gene. Retained rather than removed because there is no positive evidence against it. |
| GO:0051384 response to glucocorticoid | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Response to glucocorticoid. Glucocorticoids are classical inducers of alkaline phosphatase in osteoblastic culture systems. Reason: Describes regulation of the gene rather than the function of the protein. Not wrong, but carries no information about what the enzyme does. |
| GO:0052731 phosphocholine phosphatase activity | IEA GO_REF:0000107 | ACCEPT | Summary: Phosphocholine phosphatase activity, demonstrated on recombinant enzyme and supported in mouse by the liver steatosis and reduced serum triglyceride phenotype of TNAP-knockout animals. Reason: A genuinely new addition to the accepted substrate repertoire of this enzyme, established in 2025 with kinetics comparable to PPi hydrolysis and structural identification of the binding residues. The mouse knockout supplies the physiological readout. 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: Phosphoethanolamine phosphatase activity. Long inferred from the accumulation of phosphoethanolamine in hypophosphatasia, and now measured directly on purified enzyme. Reason: Correct and well supported. Together with the phosphocholine row this establishes that the enzyme feeds cellular choline and ethanolamine uptake for phospholipid synthesis, a function separate from mineralization. |
| GO:0055074 calcium ion homeostasis | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Calcium ion homeostasis, drawn from vascular calcification studies in which TNAP activity determines whether calcium phosphate mineral is deposited in soft tissue. Reason: Indirect. TNAP acts on phosphate-containing substrates, not on calcium; any effect on calcium is a consequence of altered calcium-phosphate deposition. Retained because the causal link to mineral deposition is real, but this is not a calcium-handling protein. |
| GO:0065010 extracellular membrane-bounded organelle | IEA GO_REF:0000107 | ACCEPT | Summary: Extracellular membrane-bounded organelle, which for this gene means the matrix vesicle: the membrane-limited vesicle released by osteoblasts and chondrocytes in which hydroxyapatite seed crystals first form. Reason: A genuine second site of action alongside the cell surface, and the is_active_in qualifier is apt. Kinetic analysis of TNAP- deficient matrix vesicles shows the enzyme's loss dominates substrate hydrolysis in that compartment. Supporting Evidence: PMID:19874193 Comparison of the catalytic efficiencies identified ATP as the main substrate hydrolyzed by WT MVs. |
| GO:0071529 cementum mineralization | IEA GO_REF:0000107 | ACCEPT | Summary: Cementum mineralization, the dental counterpart of the skeletal phenotype. Acellular cementum failure is what produces premature tooth loss in hypophosphatasia. Reason: Specific and well founded. Dental mineralization is not a peripheral aspect of this gene's biology but the presenting feature of the mildest human disease form, and the mouse is where the tissue-level defect was characterised. |
| GO:0004035 alkaline phosphatase activity | ISO GO_REF:0000119 | ACCEPT | Summary: The core molecular function. Mouse Alpl is one of the seeds behind the family-wide PAINT node for this term, and the activity is directly measured in several of the cited studies. Reason: Correct and ancestral. The family review (PANTHER:PTHR11596) found the catalytic serine and the Zn/Zn/Mg ligands conserved in all twenty-seven reviewed members, with mouse Alpl carrying serine at position 110, so the term is safe here on residue grounds as well as experimental ones. |
| GO:0004427 inorganic diphosphate phosphatase activity | ISO GO_REF:0000119 | ACCEPT | Summary: Hydrolysis of inorganic pyrophosphate, measured directly in mouse matrix vesicles and in further studies of skeletal mineralization. This is the reaction that links Alpl to bone. Reason: Core. Removing extracellular PPi lifts the brake on hydroxyapatite propagation, and the mouse knockout phenotype is the strongest evidence anywhere that this reaction matters in vivo. More specific and more informative than the generic pyrophosphatase parent. Supporting Evidence: PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0005509 calcium ion binding | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: Calcium ion binding, corresponding to the mammalian-specific structural calcium site that has no counterpart in the bacterial enzyme. Reason: Real and structurally located: the family review confirms the four calcium ligands are present as an invariant Glu-Phe-Glu-Asp set in all eight animal members examined and absent from all three microbial ones. Non-core because the site is structural rather than catalytic and does not influence phosphatase activity. |
| GO:0005886 plasma membrane | ISO GO_REF:0000119 | ACCEPT | Summary: Plasma membrane. TNAP is GPI-anchored on the outer leaflet with its catalytic domain facing outward, so this is genuinely where the enzyme acts. Reason: Correct. The family review records the PAINT node for this term as scoped to Eumetazoa and seeded partly from this gene, which is the right boundary: the bacterial members are periplasmic and the fungal ones vacuolar. |
| GO:0005886 plasma membrane | ISO GO_REF:0000119 | ACCEPT | Summary: Plasma membrane. TNAP is GPI-anchored on the outer leaflet with its catalytic domain facing outward, so this is genuinely where the enzyme acts. Reason: Correct. The family review records the PAINT node for this term as scoped to Eumetazoa and seeded partly from this gene, which is the right boundary: the bacterial members are periplasmic and the fungal ones vacuolar. |
| GO:0016462 pyrophosphatase activity | ISO GO_REF:0000119 | MODIFY | Summary: The broad parent term covering hydrolysis of any pyrophosphate bond, which also spans nucleoside triphosphatases. The experiments behind these rows measured hydrolysis of inorganic pyrophosphate specifically. Reason: GO:0004427 is a descendant of this term and is already annotated to mouse Alpl from the same experiments. Using the parent understates what was measured and blurs the distinction between destroying inorganic PPi, which is what governs mineralization, and hydrolysing a nucleotide anhydride bond. The same modification is applied in the human ALPL review. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:P05186 · ALPL SUPPORTS TRANSFER Human ALPL genuinely hydrolyses inorganic pyrophosphate, so the transfer itself is sound and the source is not at fault. The problem is the term chosen: GO:0016462 is the broad pyrophosphate-bond parent, while the measured reaction on both the human and the mouse protein is hydrolysis of inorganic diphosphate, which has its own descendant term. The human review modifies the same rows the same way. Proposed replacements: inorganic diphosphate phosphatase activity |
| GO:0033883 pyridoxal phosphatase activity | ISO GO_REF:0000119 | ACCEPT | Summary: Pyridoxal 5'-phosphate phosphatase activity. In mouse this is not an incidental substrate preference: Alpl-null mice die of seizures caused by defective vitamin B6 metabolism, which is the cleanest in vivo demonstration of the reaction's importance in the whole family. Reason: Core, and the mouse is where the causal evidence lives. Because PLP cannot cross the plasma membrane, extracellular dephosphorylation by TNAP is the obligatory step supplying cells with usable vitamin B6. |
| GO:0052731 phosphocholine phosphatase activity | ISO GO_REF:0000119 | ACCEPT | Summary: Phosphocholine phosphatase activity, demonstrated on recombinant enzyme and supported in mouse by the liver steatosis and reduced serum triglyceride phenotype of TNAP-knockout animals. Reason: A genuinely new addition to the accepted substrate repertoire of this enzyme, established in 2025 with kinetics comparable to PPi hydrolysis and structural identification of the binding residues. The mouse knockout supplies the physiological readout. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0052732 phosphoethanolamine phosphatase activity | ISO GO_REF:0000119 | ACCEPT | Summary: Phosphoethanolamine phosphatase activity. Long inferred from the accumulation of phosphoethanolamine in hypophosphatasia, and now measured directly on purified enzyme. Reason: Correct and well supported. Together with the phosphocholine row this establishes that the enzyme feeds cellular choline and ethanolamine uptake for phospholipid synthesis, a function separate from mineralization. |
| GO:0006580 ethanolamine metabolic process | IDA PMID:41145834 TNAP dephosphorylates phosphocholine and phosphoethanolamine... | ACCEPT | Summary: Ethanolamine metabolic process, following from the phosphoethanolamine phosphatase activity and supported by the knockout phenotype. Reason: Directly evidenced in mouse rather than transferred, which makes this the primary record for a process the human gene carries only by orthology. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0019695 choline metabolic process | IDA PMID:41145834 TNAP dephosphorylates phosphocholine and phosphoethanolamine... | ACCEPT | Summary: Choline metabolic process. TNAP-knockout mice develop liver steatosis and reduced serum triglycerides mirroring choline deficiency, and pharmacological inhibition lowers blood and liver choline. Reason: Core to the newly established hepatic arm of this enzyme's biology, with loss-of-function, pharmacological and enzymological support converging in the same organism. Supporting Evidence: PMID:41145834 In summary, TNAP is the phosphatase enabling cellular choline uptake during fasting, participating in hepatic lipid metabolism. |
| GO:0052731 phosphocholine phosphatase activity | IDA PMID:41145834 TNAP dephosphorylates phosphocholine and phosphoethanolamine... | ACCEPT | Summary: Phosphocholine phosphatase activity, demonstrated on recombinant enzyme and supported in mouse by the liver steatosis and reduced serum triglyceride phenotype of TNAP-knockout animals. Reason: A genuinely new addition to the accepted substrate repertoire of this enzyme, established in 2025 with kinetics comparable to PPi hydrolysis and structural identification of the binding residues. The mouse knockout supplies the physiological readout. 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: Phosphoethanolamine phosphatase activity. Long inferred from the accumulation of phosphoethanolamine in hypophosphatasia, and now measured directly on purified enzyme. Reason: Correct and well supported. Together with the phosphocholine row this establishes that the enzyme feeds cellular choline and ethanolamine uptake for phospholipid synthesis, a function separate from mineralization. Supporting Evidence: PMID:41145834 Recombinant TNAP hydrolyzes phosphocholine and phosphoethanolamine with similar efficiency than PPi. |
| GO:0005576 extracellular region | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: Extracellular region, reached when the GPI anchor is cleaved and catalytically active enzyme is released into extracellular fluid and serum. Reason: True but unspecific, and downstream of where the enzyme does its defining work. Worth keeping because circulating alkaline phosphatase is the standard clinical readout, but it is a released form rather than a functional compartment. |
| GO:0004035 alkaline phosphatase activity | ISO GO_REF:0000096 | ACCEPT | Summary: The core molecular function. Mouse Alpl is one of the seeds behind the family-wide PAINT node for this term, and the activity is directly measured in several of the cited studies. Reason: Correct and ancestral. The family review (PANTHER:PTHR11596) found the catalytic serine and the Zn/Zn/Mg ligands conserved in all twenty-seven reviewed members, with mouse Alpl carrying serine at position 110, so the term is safe here on residue grounds as well as experimental ones. |
| GO:0051384 response to glucocorticoid | ISO GO_REF:0000096 | KEEP AS NON CORE | Summary: Response to glucocorticoid. Glucocorticoids are classical inducers of alkaline phosphatase in osteoblastic culture systems. Reason: Describes regulation of the gene rather than the function of the protein. Not wrong, but carries no information about what the enzyme does. |
| GO:0065010 extracellular membrane-bounded organelle | ISO GO_REF:0000096 | ACCEPT | Summary: Extracellular membrane-bounded organelle, which for this gene means the matrix vesicle: the membrane-limited vesicle released by osteoblasts and chondrocytes in which hydroxyapatite seed crystals first form. Reason: A genuine second site of action alongside the cell surface, and the is_active_in qualifier is apt. Kinetic analysis of TNAP- deficient matrix vesicles shows the enzyme's loss dominates substrate hydrolysis in that compartment. Supporting Evidence: PMID:19874193 Comparison of the catalytic efficiencies identified ATP as the main substrate hydrolyzed by WT MVs. |
| GO:0004427 inorganic diphosphate phosphatase activity | EXP PMID:19874193 Kinetic analysis of substrate utilization by native and TNAP... | ACCEPT | Summary: Hydrolysis of inorganic pyrophosphate, measured directly in mouse matrix vesicles and in further studies of skeletal mineralization. This is the reaction that links Alpl to bone. Reason: Core. Removing extracellular PPi lifts the brake on hydroxyapatite propagation, and the mouse knockout phenotype is the strongest evidence anywhere that this reaction matters in vivo. More specific and more informative than the generic pyrophosphatase parent. Supporting Evidence: PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0004427 inorganic diphosphate phosphatase activity | EXP PMID:23942722 Effects of pH on the production of phosphate and pyrophospha... | ACCEPT | Summary: Hydrolysis of inorganic pyrophosphate, measured directly in mouse matrix vesicles and in further studies of skeletal mineralization. This is the reaction that links Alpl to bone. Reason: Core. Removing extracellular PPi lifts the brake on hydroxyapatite propagation, and the mouse knockout phenotype is the strongest evidence anywhere that this reaction matters in vivo. More specific and more informative than the generic pyrophosphatase parent. Supporting Evidence: PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0004427 inorganic diphosphate phosphatase activity | EXP PMID:29174347 Discovery of 5-((5-chloro-2-methoxyphenyl)sulfonamido)nicoti... | ACCEPT | Summary: Hydrolysis of inorganic pyrophosphate, measured directly in mouse matrix vesicles and in further studies of skeletal mineralization. This is the reaction that links Alpl to bone. Reason: Core. Removing extracellular PPi lifts the brake on hydroxyapatite propagation, and the mouse knockout phenotype is the strongest evidence anywhere that this reaction matters in vivo. More specific and more informative than the generic pyrophosphatase parent. Supporting Evidence: PMID:19874193 We conclude that TNAP is the enzyme that hydrolyzes both ATP and PP(i) in the MV compartment. |
| GO:0005886 plasma membrane | ISS GO_REF:0000024 | ACCEPT | Summary: Plasma membrane. TNAP is GPI-anchored on the outer leaflet with its catalytic domain facing outward, so this is genuinely where the enzyme acts. Reason: Correct. The family review records the PAINT node for this term as scoped to Eumetazoa and seeded partly from this gene, which is the right boundary: the bacterial members are periplasmic and the fungal ones vacuolar. |
| GO:0016887 ATP hydrolysis activity | EXP PMID:19874193 Kinetic analysis of substrate utilization by native and TNAP... | KEEP AS NON CORE | Summary: ATP hydrolysis activity. The enzyme does hydrolyse ATP, and in osteoblast-derived matrix vesicles ATP was the main substrate hydrolysed, with TNAP the responsible enzyme. Reason: The chemistry is real but the term carries an unhelpful connotation: it normally labels ATPases that couple hydrolysis to work, whereas TNAP strips the terminal phosphate as a promiscuous phosphomonoesterase with no energy coupling. Retained as non-core to record the ectonucleotidase capability without implying it is an ATPase. Supporting Evidence: PMID:19874193 The lack of TNAP had the most pronounced effect on the hydrolysis of all physiologic substrates. |
| GO:0033883 pyridoxal phosphatase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Pyridoxal 5'-phosphate phosphatase activity. In mouse this is not an incidental substrate preference: Alpl-null mice die of seizures caused by defective vitamin B6 metabolism, which is the cleanest in vivo demonstration of the reaction's importance in the whole family. Reason: Core, and the mouse is where the causal evidence lives. Because PLP cannot cross the plasma membrane, extracellular dephosphorylation by TNAP is the obligatory step supplying cells with usable vitamin B6. |
| GO:0043262 ADP phosphatase activity | EXP PMID:19874193 Kinetic analysis of substrate utilization by native and TNAP... | KEEP AS NON CORE | Summary: ADP phosphatase activity, the middle step of stepwise extracellular ATP degradation, measured in matrix vesicles. Reason: Genuine but ancillary: purinergic nucleotide turnover is shared with the ENPP, CD39 and CD73 systems and is not the reaction whose loss produces the knockout phenotype. |
| GO:0052732 phosphoethanolamine phosphatase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Phosphoethanolamine phosphatase activity. Long inferred from the accumulation of phosphoethanolamine in hypophosphatasia, and now measured directly on purified enzyme. Reason: Correct and well supported. Together with the phosphocholine row this establishes that the enzyme feeds cellular choline and ethanolamine uptake for phospholipid synthesis, a function separate from mineralization. |
| GO:0030282 bone mineralization | IMP PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:12082181 Mutations in the TNAP gene result in the inborn error of metabolism known as hypophosphatasia, characterized by poorly mineralized bones, spontaneous fractures, and elevated extracellular concentrations of inorganic pyrophosphate (PP(i)). |
| GO:0030282 bone mineralization | IGI PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:12082181 Mutations in the TNAP gene result in the inborn error of metabolism known as hypophosphatasia, characterized by poorly mineralized bones, spontaneous fractures, and elevated extracellular concentrations of inorganic pyrophosphate (PP(i)). |
| GO:0034516 response to vitamin B6 | IMP PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | KEEP AS NON CORE | Summary: Response to vitamin B6, from the knockout studies in which pyridoxine supplementation modifies the seizure phenotype. Reason: The substantive B6 connection is captured better and more mechanistically by the pyridoxal phosphatase activity and PLP metabolic process terms. This row adds the stimulus-response framing only. |
| GO:0034516 response to vitamin B6 | IGI PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | KEEP AS NON CORE | Summary: Response to vitamin B6, from the knockout studies in which pyridoxine supplementation modifies the seizure phenotype. Reason: The substantive B6 connection is captured better and more mechanistically by the pyridoxal phosphatase activity and PLP metabolic process terms. This row adds the stimulus-response framing only. |
| GO:0055062 phosphate ion homeostasis | IMP PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | KEEP AS NON CORE | Summary: Phosphate ion homeostasis. TNAP liberates inorganic phosphate from PPi and phosphomonoesters, contributing to the local PPi/Pi ratio that governs mineralization. Reason: Directionally correct but framed at the wrong scale. The enzyme's effect is on the local extracellular PPi/Pi balance at a mineralizing front, not on organismal phosphate homeostasis, which is governed by FGF23, PTH and renal transporters. Serum phosphate is characteristically normal or high in hypophosphatasia. |
| GO:0055062 phosphate ion homeostasis | IGI PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | KEEP AS NON CORE | Summary: Phosphate ion homeostasis. TNAP liberates inorganic phosphate from PPi and phosphomonoesters, contributing to the local PPi/Pi ratio that governs mineralization. Reason: Directionally correct but framed at the wrong scale. The enzyme's effect is on the local extracellular PPi/Pi balance at a mineralizing front, not on organismal phosphate homeostasis, which is governed by FGF23, PTH and renal transporters. Serum phosphate is characteristically normal or high in hypophosphatasia. |
| GO:1904383 response to sodium phosphate | IMP PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | KEEP AS NON CORE | Summary: Response to sodium phosphate, from experiments in which phosphate exposure altered alkaline phosphatase expression or activity. Reason: Records responsiveness of the gene to a stimulus rather than a function of the protein. Accurate but uninformative about mechanism, and easily mistaken for evidence that the enzyme handles phosphate homeostasis. |
| GO:1904383 response to sodium phosphate | IGI PMID:12082181 Tissue-nonspecific alkaline phosphatase and plasma cell memb... | KEEP AS NON CORE | Summary: Response to sodium phosphate, from experiments in which phosphate exposure altered alkaline phosphatase expression or activity. Reason: Records responsiveness of the gene to a stimulus rather than a function of the protein. Accurate but uninformative about mechanism, and easily mistaken for evidence that the enzyme handles phosphate homeostasis. |
| GO:0030282 bone mineralization | IMP PMID:15920156 Sustained osteomalacia of long bones despite major improveme... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:15920156 Thus, the osteomalacia of Akp2-/- mice and the hypomineralized phenotype of the long bones of Enpp1-/- mice are not rescued by simultaneous deletion of TNAP and NPP1 functions. |
| GO:0030282 bone mineralization | IGI PMID:15920156 Sustained osteomalacia of long bones despite major improveme... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:15920156 Thus, the osteomalacia of Akp2-/- mice and the hypomineralized phenotype of the long bones of Enpp1-/- mice are not rescued by simultaneous deletion of TNAP and NPP1 functions. |
| GO:0055062 phosphate ion homeostasis | IDA PMID:21490328 Extracellular pyrophosphate metabolism and calcification in ... | KEEP AS NON CORE | Summary: Phosphate ion homeostasis. TNAP liberates inorganic phosphate from PPi and phosphomonoesters, contributing to the local PPi/Pi ratio that governs mineralization. Reason: Directionally correct but framed at the wrong scale. The enzyme's effect is on the local extracellular PPi/Pi balance at a mineralizing front, not on organismal phosphate homeostasis, which is governed by FGF23, PTH and renal transporters. Serum phosphate is characteristically normal or high in hypophosphatasia. |
| GO:0055062 phosphate ion homeostasis | IMP PMID:21490328 Extracellular pyrophosphate metabolism and calcification in ... | KEEP AS NON CORE | Summary: Phosphate ion homeostasis. TNAP liberates inorganic phosphate from PPi and phosphomonoesters, contributing to the local PPi/Pi ratio that governs mineralization. Reason: Directionally correct but framed at the wrong scale. The enzyme's effect is on the local extracellular PPi/Pi balance at a mineralizing front, not on organismal phosphate homeostasis, which is governed by FGF23, PTH and renal transporters. Serum phosphate is characteristically normal or high in hypophosphatasia. |
| GO:0055074 calcium ion homeostasis | IDA PMID:21490328 Extracellular pyrophosphate metabolism and calcification in ... | KEEP AS NON CORE | Summary: Calcium ion homeostasis, drawn from vascular calcification studies in which TNAP activity determines whether calcium phosphate mineral is deposited in soft tissue. Reason: Indirect. TNAP acts on phosphate-containing substrates, not on calcium; any effect on calcium is a consequence of altered calcium-phosphate deposition. Retained because the causal link to mineral deposition is real, but this is not a calcium-handling protein. |
| GO:0140928 inhibition of non-skeletal tissue mineralization | IDA PMID:21490328 Extracellular pyrophosphate metabolism and calcification in ... | REMOVE | Summary: This is the source annotation behind the directionally inverted transfers into human, and reviewing it here is the point of doing the mouse gene. The term asserts a homeostatic process that acts by preventing mineralization of non-skeletal tissue. The cited paper shows the opposite for TNAP: overexpressing it increased calcification of cultured aortas, and inhibiting it reduced pyrophosphate hydrolysis by half. The only inhibitory role the paper attributes is to pyrophosphate itself, not to the enzyme that destroys it. Reason: TNAP degrades extracellular pyrophosphate, the endogenous inhibitor of hydroxyapatite propagation, so it promotes rather than prevents ectopic mineralization. The genes that genuinely perform this process, ENPP1 and ANK, are the other arms of the same paper and are correctly annotated to it. The likely origin of the error is the abstract's closing sentence, which credits an inhibitory role to locally produced pyrophosphate; read quickly, that can be taken as crediting TNAP. Independent human-relevant evidence points the same way: a selective TNAP inhibitor attenuates ectopic calcification in Abcc6-null mice. Either a NOT qualifier or a new term for the promoting direction would capture the real relationship. The human IEA that descends from this row was removed in the ALPL review, and the family review records the term as NOT_APPLICABLE across PANTHER:PTHR11596. Supporting Evidence: PMID:21490328 Overexpression of TNAP increased calcification of cultured aortas. PMID:21490328 The results show that smooth muscle NPP1 and TNAP control vascular calcification through effects on synthesis and hydrolysis of ePP i , indicating an important inhibitory role of locally produced PP i . |
| GO:0140928 inhibition of non-skeletal tissue mineralization | IMP PMID:21490328 Extracellular pyrophosphate metabolism and calcification in ... | REMOVE | Summary: This is the source annotation behind the directionally inverted transfers into human, and reviewing it here is the point of doing the mouse gene. The term asserts a homeostatic process that acts by preventing mineralization of non-skeletal tissue. The cited paper shows the opposite for TNAP: overexpressing it increased calcification of cultured aortas, and inhibiting it reduced pyrophosphate hydrolysis by half. The only inhibitory role the paper attributes is to pyrophosphate itself, not to the enzyme that destroys it. Reason: TNAP degrades extracellular pyrophosphate, the endogenous inhibitor of hydroxyapatite propagation, so it promotes rather than prevents ectopic mineralization. The genes that genuinely perform this process, ENPP1 and ANK, are the other arms of the same paper and are correctly annotated to it. The likely origin of the error is the abstract's closing sentence, which credits an inhibitory role to locally produced pyrophosphate; read quickly, that can be taken as crediting TNAP. Independent human-relevant evidence points the same way: a selective TNAP inhibitor attenuates ectopic calcification in Abcc6-null mice. Either a NOT qualifier or a new term for the promoting direction would capture the real relationship. The human IEA that descends from this row was removed in the ALPL review, and the family review records the term as NOT_APPLICABLE across PANTHER:PTHR11596. A second, independent problem is specific to this IMP row: its WITH/FROM cites MGI:1856651 and MGI:2385534, which resolve to the Ank(ank) and Enpp1(tm1Gdg) alleles -- the ank/ank and Enpp1-null strains of the same study. The mutant phenotypes on which this Alpl annotation rests therefore belong to other genes, ones that genuinely make or export pyrophosphate and are correctly annotated to this term themselves. Supporting Evidence: PMID:21490328 Overexpression of TNAP increased calcification of cultured aortas. PMID:21490328 The results show that smooth muscle NPP1 and TNAP control vascular calcification through effects on synthesis and hydrolysis of ePP i , indicating an important inhibitory role of locally produced PP i . |
| GO:1904383 response to sodium phosphate | IDA PMID:23523568 A protective role for FGF-23 in local defence against disrup... | KEEP AS NON CORE | Summary: Response to sodium phosphate, from experiments in which phosphate exposure altered alkaline phosphatase expression or activity. Reason: Records responsiveness of the gene to a stimulus rather than a function of the protein. Accurate but uninformative about mechanism, and easily mistaken for evidence that the enzyme handles phosphate homeostasis. |
| GO:0005509 calcium ion binding | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Calcium ion binding, corresponding to the mammalian-specific structural calcium site that has no counterpart in the bacterial enzyme. Reason: Real and structurally located: the family review confirms the four calcium ligands are present as an invariant Glu-Phe-Glu-Asp set in all eight animal members examined and absent from all three microbial ones. Non-core because the site is structural rather than catalytic and does not influence phosphatase activity. |
| GO:0016462 pyrophosphatase activity | IDA PMID:29174347 Discovery of 5-((5-chloro-2-methoxyphenyl)sulfonamido)nicoti... | MODIFY | Summary: The broad parent term covering hydrolysis of any pyrophosphate bond, which also spans nucleoside triphosphatases. The experiments behind these rows measured hydrolysis of inorganic pyrophosphate specifically. Reason: GO:0004427 is a descendant of this term and is already annotated to mouse Alpl from the same experiments. Using the parent understates what was measured and blurs the distinction between destroying inorganic PPi, which is what governs mineralization, and hydrolysing a nucleotide anhydride bond. The same modification is applied in the human ALPL review. Proposed replacements: inorganic diphosphate phosphatase activity |
| GO:0030282 bone mineralization | IMP PMID:10620060 Alkaline phosphatase knock-out mice recapitulate the metabol... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:10620060 Our findings demonstrate that TNSALP knock-out mice are a good model for the infantile form of hypophosphatasia and provide compelling evidence for an important role for TNSALP in postnatal development and mineralization of the murine skeleton. |
| GO:0030282 bone mineralization | IMP PMID:11028439 Functional characterization of osteoblasts and osteoclasts f... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. |
| GO:0030282 bone mineralization | IMP PMID:14982838 Impaired calcification around matrix vesicles of growth plat... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:14982838 These data suggest that hypomineralization in TNAP-deficient mice results primarily from an inability of initial mineral crystals within MVs to self-nucleate and to proliferate beyond the protective confines of the MV membrane. |
| GO:0030282 bone mineralization | IMP PMID:20684022 Loss of skeletal mineralization by the simultaneous ablation... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:20684022 Here we show that PHOSPHO1, a phosphatase with specificity for phosphoethanolamine and phosphocholine, plays a functional role in the initiation of calcification and that ablation of PHOSPHO1 and TNAP function prevents skeletal mineralization. |
| GO:0030282 bone mineralization | IMP PMID:26457330 The Functional co-operativity of Tissue-Nonspecific Alkaline... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. Supporting Evidence: PMID:26457330 Tissue-nonspecific alkaline phosphatase (TNAP) and PHOSPHO1 are indispensable for bone and cartilage mineralization but their functional relationship in the mineralization process remains unclear. |
| GO:0030282 bone mineralization | IMP PMID:9056646 Inactivation of two mouse alkaline phosphatase genes and est... | ACCEPT | Summary: Bone mineralization, the best-supported process annotation for this gene and the one with the deepest evidence base: eleven rows drawn from eight separate mouse studies, including single and compound knockouts with Phospho1 and Enpp1. Reason: Core, and this is the organism in which the causal chain was established. Alpl-null mice reproduce hypophosphatasia, and the compound ablations dissect the division of labour between TNAP and PHOSPHO1 in initiating versus propagating mineral. The family review scopes this term to Euteleostomi on a PAINT node seeded from this very gene. |
| GO:0042822 pyridoxal 5'-phosphate metabolic process | IDA PMID:7550313 Mice lacking tissue non-specific alkaline phosphatase die fr... | ACCEPT | Summary: The process-level counterpart of the PLP phosphatase activity, from the knockout study showing that mice lacking tissue- nonspecific alkaline phosphatase die from seizures due to defective vitamin B6 metabolism. Reason: Core. This is the annotation that the human ALPL record inherits and that explains pyridoxine-responsive seizures in infantile hypophosphatasia; here it rests on a direct mouse loss-of-function phenotype rather than on inference. |
| GO:0120162 positive regulation of cold-induced thermogenesis | IDA PMID:33981039 Mitochondrial TNAP controls thermogenesis by hydrolysis of p... | ACCEPT | Summary: Positive regulation of cold-induced thermogenesis. TNAP expression is powerfully induced by cold exposure, and genetic ablation in adipocytes reduces energy expenditure and causes rapid-onset obesity with no change in movement or feeding. Reason: A genuine second role for this enzyme, established here by adipocyte-specific knockout with a whole-animal metabolic phenotype. Core for mouse even though the human counterpart remains an orthology inference. Supporting Evidence: PMID:33981039 In addition, genetic ablation of TNAP in adipocytes reduces whole-body energy expenditure and leads to rapid-onset obesity in mice, with no change in movement or feeding behaviour. |
| GO:0055074 calcium ion homeostasis | ISO PMID:28592560 Ectopic calcification in pseudoxanthoma elasticum responds t... | KEEP AS NON CORE | Summary: Calcium ion homeostasis, drawn from vascular calcification studies in which TNAP activity determines whether calcium phosphate mineral is deposited in soft tissue. Reason: Indirect. TNAP acts on phosphate-containing substrates, not on calcium; any effect on calcium is a consequence of altered calcium-phosphate deposition. Retained because the causal link to mineral deposition is real, but this is not a calcium-handling protein. |
| GO:0055074 calcium ion homeostasis | IMP PMID:28592560 Ectopic calcification in pseudoxanthoma elasticum responds t... | KEEP AS NON CORE | Summary: Calcium ion homeostasis, drawn from vascular calcification studies in which TNAP activity determines whether calcium phosphate mineral is deposited in soft tissue. Reason: Indirect. TNAP acts on phosphate-containing substrates, not on calcium; any effect on calcium is a consequence of altered calcium-phosphate deposition. Retained because the causal link to mineral deposition is real, but this is not a calcium-handling protein. |
| GO:0050187 phosphoamidase activity | IDA PMID:33981039 Mitochondrial TNAP controls thermogenesis by hydrolysis of p... | ACCEPT | Summary: Phosphoamidase activity, defined narrowly as hydrolysis of N-phosphocreatine to creatine and phosphate. In mouse this is directly demonstrated: thermogenic fat cells have robust phosphocreatine phosphatase activity attributable to TNAP. Reason: Accepted here on direct evidence, in contrast to the human record where the same term rests only on similarity to this gene. This is the annotation that grounds the whole futile creatine cycle story, and the mouse is where it was established. Supporting Evidence: PMID:33981039 Thermogenic fat cells have robust phosphocreatine phosphatase activity, which is attributed to tissue-nonspecific alkaline phosphatase (TNAP). |
| GO:0140651 futile creatine cycle | IDA PMID:33981039 Mitochondrial TNAP controls thermogenesis by hydrolysis of p... | ACCEPT | Summary: Futile creatine cycle. TNAP hydrolyses phosphocreatine to initiate a cycle of creatine dephosphorylation and rephosphorylation that dissipates the phosphate bond energy as heat. Reason: Directly demonstrated in this organism, with inhibition in isolated mitochondria abolishing futile creatine cycling and adipocyte-specific ablation reducing whole-body energy expenditure. The human annotations for this process are orthology transfers from this evidence. Supporting Evidence: PMID:33981039 TNAP hydrolyses phosphocreatine to initiate a futile cycle of creatine dephosphorylation and phosphorylation. |
| GO:0005758 mitochondrial intermembrane space | IDA PMID:33981039 Mitochondrial TNAP controls thermogenesis by hydrolysis of p... | ACCEPT | Summary: Mitochondrial intermembrane space. Unlike in other cells, TNAP in thermogenic fat cells localises to mitochondria, which is where futile creatine cycling occurs. Reason: Topologically unusual for a GPI-anchored protein and therefore worth stating carefully, but this is the direct observation on which the human ISS and IEA rows depend. Accepting it here while keeping the human rows non-core is the correct asymmetry: the evidence is in this organism. Supporting Evidence: PMID:33981039 Unlike in other cells, TNAP in thermogenic fat cells is localized to the mitochondria, where futile creatine cycling occurs. file:mouse/Alpl/Alpl-deep-research-falcon.md Biochemical purification found Alpl/TNAP **sevenfold enriched** in the active mitochondrial phosphocreatine-phosphatase fraction. |
| GO:0031966 mitochondrial membrane | IDA PMID:33981039 Mitochondrial TNAP controls thermogenesis by hydrolysis of p... | ACCEPT | Summary: Mitochondrial membrane, the companion localisation from the same study, with TNAP described as tethered to mitochondrial membranes in thermogenic adipocytes. Reason: Same basis and same assessment as the intermembrane space row: direct evidence in this organism, restricted to one cell type but not therefore doubtful. Supporting Evidence: PMID:33981039 TNAP expression is powerfully induced when mice are exposed to cold conditions, and its inhibition in isolated mitochondria leads to a loss of futile creatine cycling. |
| GO:0031012 extracellular matrix | IDA PMID:19874193 Kinetic analysis of substrate utilization by native and TNAP... | KEEP AS NON CORE | Summary: Extracellular matrix, from the matrix vesicle kinetics work. The enzyme acts at the cell-matrix interface where nascent mineral forms. Reason: True as a description of where the enzyme operates, but loose as a located_in assertion for a GPI-anchored membrane protein. The precise statements are the plasma membrane and the matrix vesicle membrane, both separately annotated. |
| GO:0005515 protein binding | IPI PMID:23055941 RAB-like 2 has an essential role in male fertility, sperm in... | MARK AS OVER ANNOTATED | Summary: A bare protein binding annotation with no functional interpretation attached. Reason: Uninformative by the project's curation standard. Unlike the family's structurally load-bearing homodimer, which is proposed as a separate annotation below, this row names no partner biology and supports no inference about what the enzyme does. If the interaction proves meaningful it should be recorded with a specific term. |
| GO:0065010 extracellular membrane-bounded organelle | IDA PMID:19874193 Kinetic analysis of substrate utilization by native and TNAP... | ACCEPT | Summary: Extracellular membrane-bounded organelle, which for this gene means the matrix vesicle: the membrane-limited vesicle released by osteoblasts and chondrocytes in which hydroxyapatite seed crystals first form. Reason: A genuine second site of action alongside the cell surface, and the is_active_in qualifier is apt. Kinetic analysis of TNAP- deficient matrix vesicles shows the enzyme's loss dominates substrate hydrolysis in that compartment. Supporting Evidence: PMID:19874193 Comparison of the catalytic efficiencies identified ATP as the main substrate hydrolyzed by WT MVs. |
| GO:0001958 endochondral ossification | IMP PMID:20684022 Loss of skeletal mineralization by the simultaneous ablation... | ACCEPT | Summary: Endochondral ossification, from the compound Phospho1/Alpl ablation study showing loss of skeletal mineralization. Reason: A more specific developmental framing of the skeletal phenotype than bone mineralization alone, and appropriately qualified as acts_upstream_of_or_within rather than as a direct participation claim. Supporting Evidence: PMID:20684022 Here we show that PHOSPHO1, a phosphatase with specificity for phosphoethanolamine and phosphocholine, plays a functional role in the initiation of calcification and that ablation of PHOSPHO1 and TNAP function prevents skeletal mineralization. |
| GO:0016462 pyrophosphatase activity | ISO GO_REF:0000008 | MODIFY | Summary: The broad parent term covering hydrolysis of any pyrophosphate bond, which also spans nucleoside triphosphatases. The experiments behind these rows measured hydrolysis of inorganic pyrophosphate specifically. Reason: GO:0004427 is a descendant of this term and is already annotated to mouse Alpl from the same experiments. Using the parent understates what was measured and blurs the distinction between destroying inorganic PPi, which is what governs mineralization, and hydrolysing a nucleotide anhydride bond. The same modification is applied in the human ALPL review. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:P05186 · ALPL SUPPORTS TRANSFER Human ALPL genuinely hydrolyses inorganic pyrophosphate, so the transfer itself is sound and the source is not at fault. The problem is the term chosen: GO:0016462 is the broad pyrophosphate-bond parent, while the measured reaction on both the human and the mouse protein is hydrolysis of inorganic diphosphate, which has its own descendant term. The human review modifies the same rows the same way. Proposed replacements: inorganic diphosphate phosphatase activity |
| GO:0016462 pyrophosphatase activity | IMP PMID:19874193 Kinetic analysis of substrate utilization by native and TNAP... | MODIFY | Summary: The broad parent term covering hydrolysis of any pyrophosphate bond, which also spans nucleoside triphosphatases. The experiments behind these rows measured hydrolysis of inorganic pyrophosphate specifically. Reason: GO:0004427 is a descendant of this term and is already annotated to mouse Alpl from the same experiments. Using the parent understates what was measured and blurs the distinction between destroying inorganic PPi, which is what governs mineralization, and hydrolysing a nucleotide anhydride bond. The same modification is applied in the human ALPL review. Proposed replacements: inorganic diphosphate phosphatase activity |
| GO:0003006 developmental process involved in reproduction | IGI PMID:17540358 Cell type-autonomous and non-autonomous requirements for Dmr... | KEEP AS NON CORE | Summary: Developmental process involved in reproduction, from a genetic interaction study. Alkaline phosphatase is a long-standing marker of primordial germ cells in mouse. Reason: Plausible in outline but very general, and the connection to the enzyme's chemistry is not established. Kept as non-core: an IGI to a broad developmental term is a weak basis for a functional claim, and nothing else in the record supports a reproductive role. |
| GO:0004035 alkaline phosphatase activity | IDA PMID:10787428 Localization of the murine Niemann-Pick C1 protein to two di... | ACCEPT | Summary: The term is correct but the citation is a marker-enzyme use rather than a characterisation. The cited paper localises the murine Niemann-Pick C1 protein to two intracellular compartments; alkaline phosphatase appears in such studies as the standard plasma membrane marker enzyme in fractionation assays. Reason: Accepted because the assertion is beyond doubt for this gene and is supported independently many times over, so nothing rests on this citation. It is recorded as a citation problem rather than a functional one: measuring a marker enzyme's activity to identify a fraction demonstrates the activity only incidentally and is thin ground for an IDA. Flagged in the reference review. |
| GO:0005886 plasma membrane | IDA PMID:10787428 Localization of the murine Niemann-Pick C1 protein to two di... | ACCEPT | Summary: Plasma membrane localisation from the same Niemann-Pick C1 fractionation study, where alkaline phosphatase served as the plasma membrane marker. Reason: Better supported by this citation than the activity row is: using an enzyme as a compartment marker presupposes and in practice confirms its localisation to that compartment. The conclusion is also independently established, so the row is sound even though the paper is not about this gene. |
| GO:0004035 alkaline phosphatase activity | ISO PMID:2133555 Two alkaline phosphatase genes are expressed during early de... | ACCEPT | Summary: Alkaline phosphatase activity, cited from the mouse preimplantation embryo expression study with an ISO evidence code. Reason: The term is correct and independently supported. The pairing is odd -- an orthology-inferred code attached to a same-species expression paper -- and the underlying study measured transcripts rather than activity, so this row adds no independent experimental weight. Accepted on the strength of the other evidence rather than on this citation. |
| GO:0046677 response to antibiotic | IDA PMID:2133555 Two alkaline phosphatase genes are expressed during early de... | UNDECIDED | Summary: Response to antibiotic, cited from a study of alkaline phosphatase gene expression in mouse preimplantation embryos. The cached record does not mention antibiotics, selection agents or drug treatment anywhere, and nothing in the abstract suggests an antibiotic exposure experiment. Reason: Marked undecided rather than removed because only the abstract is cached and the curator may have drawn on methods the abstract does not describe, such as a selection agent used in the cell lines. But the annotation should not be relied on: it is unsupported by everything visible in the cached record and it is the second questionable annotation traced to this same paper, which is also flagged in the human ALPP review for supplying an IDA for enzyme activity from a mouse transcript survey. |
| GO:0004035 alkaline phosphatase activity | IDA PMID:18031938 The ectonucleotidases alkaline phosphatase and nucleoside tr... | ACCEPT | Summary: The core molecular function. Mouse Alpl is one of the seeds behind the family-wide PAINT node for this term, and the activity is directly measured in several of the cited studies. Reason: Correct and ancestral. The family review (PANTHER:PTHR11596) found the catalytic serine and the Zn/Zn/Mg ligands conserved in all twenty-seven reviewed members, with mouse Alpl carrying serine at position 110, so the term is safe here on residue grounds as well as experimental ones. |
| GO:0004035 alkaline phosphatase activity | IDA PMID:7533563 Stage-specific expression of alkaline phosphatase during neu... | ACCEPT | Summary: The core molecular function. Mouse Alpl is one of the seeds behind the family-wide PAINT node for this term, and the activity is directly measured in several of the cited studies. Reason: Correct and ancestral. The family review (PANTHER:PTHR11596) found the catalytic serine and the Zn/Zn/Mg ligands conserved in all twenty-seven reviewed members, with mouse Alpl carrying serine at position 110, so the term is safe here on residue grounds as well as experimental ones. |
| GO:0005886 plasma membrane | IDA PMID:7533563 Stage-specific expression of alkaline phosphatase during neu... | ACCEPT | Summary: Plasma membrane. TNAP is GPI-anchored on the outer leaflet with its catalytic domain facing outward, so this is genuinely where the enzyme acts. Reason: Correct. The family review records the PAINT node for this term as scoped to Eumetazoa and seeded partly from this gene, which is the right boundary: the bacterial members are periplasmic and the fungal ones vacuolar. |
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Download this section (compressed HTML)Q: Is mitochondrial localisation of TNAP in thermogenic adipocytes reproducible in human cells? Every human annotation for this compartment and for phosphocreatine hydrolysis is an orthology transfer from the mouse work, and a GPI-anchored ectoenzyme reaching the mitochondrial intermembrane space is topologically unusual enough that independent confirmation would be valuable.
Q: How is the substrate hierarchy set in vivo? Recombinant enzyme hydrolyses phosphocholine and phosphoethanolamine about as efficiently as pyrophosphate, yet the knockout phenotype is dominated by skeletal disease and B6-dependent seizures. Is the ordering set by local substrate concentration, by compartmentalisation on matrix vesicles versus the hepatocyte surface, or by competition with other ectophosphatases?
Q: How many species carry the directionally inverted GO:0140928 annotation propagated from this gene, and does correcting it here propagate the fix? The term currently reaches more than thirty organisms by orthology from these two mouse rows, so the mouse record is the leverage point.
Experiment: Test the direction explicitly in mouse vascular smooth muscle by overexpressing and separately inhibiting TNAP under calcifying conditions and measuring both mineral deposition and extracellular pyrophosphate, alongside Enpp1-null and ank/ank controls from the same study design. This restates the original experiment with the direction as the primary readout rather than as a secondary observation, and would settle the annotation on its own evidence.
Hypothesis: TNAP promotes rather than prevents ectopic mineralization, so the GO:0140928 annotation on this gene is directionally wrong.
Type: cell and tissue calcification assay
Experiment: Build knock-in mice carrying substitutions that impair one substrate branch while sparing the others, guided by the human hypophosphatasia alleles that already dissociate pyrophosphate from pyridoxal phosphate activity, and phenotype for skeletal mineralization, seizure susceptibility, hepatic lipid handling and cold-induced energy expenditure. Separating the branches in one organism would show whether the three core functions recorded here are truly independent or share a rate-limiting step.
Hypothesis: The mineralization, vitamin B6 and futile creatine cycle roles can be separated genetically.
Type: knock-in mouse allelic series
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