CRISPLD1 is a secreted, disulfide-rich CAP-superfamily protein containing an N-terminal SCP/CAP domain and two C-terminal LCCL domains. Its direct molecular target and biochemical activity remain unknown. In human induced-pluripotent-stem-cell derived cardiomyocytes, CRISPR/Cas9 loss of function increases calcium-transient amplitude and alters rise and decay kinetics, supporting a role for extracellular CRISPLD1 in restraining cardiomyocyte calcium cycling. CRISPLD1 expression rises during the transition from pressure-overload hypertrophy to heart failure. Human genetic data provide only weak, interaction-dependent evidence for a craniofacial developmental role, while parotid-saliva and prostatic-fluid proteomes detect the protein in exosome-enriched extracellular fractions.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005576 extracellular region | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER phylogenetic inference places CRISPLD1 in the extracellular region. This agrees with the N-terminal signal peptide, the reviewed UniProt secretion statement, and detection in two extracellular-fluid proteomic datasets. Reason: Extracellular localization is a well-supported defining feature of CRISPLD1 and is conserved among the secreted CAP/LCCL family members represented at the PAINT node. The broad term is appropriate because the physiological extracellular microenvironment of CRISPLD1 action is not yet resolved. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000036124 · CAP-family ancestral node SUPPORTS TRANSFER Multiple secreted CAP-family seeds support extracellular localization, and CRISPLD1 independently has a signal peptide and secretion evidence. Supporting Evidence: file:human/CRISPLD1/CRISPLD1-uniprot.txt CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}. PMID:32146539 The candidate gene cysteine-rich secretory protein LCCL domain containing 1 (CRISPLD1) is secreted |
| GO:0060090 molecular adaptor activity | IBA GO_REF:0000033 | REMOVE | Summary: The PAINT molecular-adaptor inference traces to a single seed, mouse Glipr1l1, whose direct evidence is specific to an outer-acrosomal-membrane sperm complex. No CRISPLD1 study identifies macromolecules that it bridges or demonstrates an adaptor mechanism. Reason: This is an unsafe transfer across divergent CAP-family paralogs. Mouse Glipr1l1 is a 236-aa CAP-only reproductive protein, whereas CRISPLD1 is a 500-aa secreted SF9 protein with a CAP domain plus two LCCL domains. The human cardiomyocyte study establishes a calcium-transient phenotype but explicitly leaves the molecular mechanism unresolved; it does not rescue the adaptor inference. Retaining this MF would convert a tissue-specific source mechanism into an unsupported CRISPLD1 molecular activity. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE CONTEXT OR TISSUE MISMATCH Sources checked: MGI:MGI:1916536 · Glipr1l1 (mouse) SUPPORTS SOURCE BUT NOT TARGET Direct adaptor evidence is embedded in a sperm outer-acrosomal-membrane process and does not establish the activity for CRISPLD1. PANTHER:PTN000036124 · CAP-family ancestral node SUPPORTS SOURCE BUT NOT TARGET The node has only the Glipr1l1 adaptor seed and spans proteins with strongly divergent architectures and physiological contexts. Supporting Evidence: file:human/CRISPLD1/CRISPLD1-notes.md The sole PANTHER seed for GO:0060090 is therefore biologically specific to a divergent reproductive CAP paralog and does not support transfer to CRISPLD1 PMID:32146539 However, the detailed underlying molecular mechanisms remain to be investigated in the future. |
| GO:0005576 extracellular region | IEA GO_REF:0000120 | ACCEPT | Summary: Combined electronic inference places CRISPLD1 in the extracellular region from its InterPro family assignment and UniProt subcellular-location mapping. Reason: The inference is independently supported by CRISPLD1's signal peptide, reviewed secretion statement, and extracellular-fluid proteomic detections. Although broad, extracellular region is the best evidence-bounded location for its calcium-regulatory role because a specific receptor-facing compartment is unknown. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR018244 · Allergen V5/Tpx-1 conserved site SUPPORTS TRANSFER UniProtKB-SubCell:SL-0243 · secreted subcellular-location mapping SUPPORTS TRANSFER Supporting Evidence: file:human/CRISPLD1/CRISPLD1-uniprot.txt FT SIGNAL 1..23 file:human/CRISPLD1/CRISPLD1-uniprot.txt CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}. |
| GO:0060325 face morphogenesis | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: The ARBA electronic annotation projects face morphogenesis to CRISPLD1. Its underlying biological context is a human cleft-lip/palate association study with developmental expression observations, not a direct CRISPLD1 perturbation. Reason: A craniofacial role is plausible but not established. The full paper reports only one marginally transmitted CRISPLD1 SNP, states that CRISPLD1 variation alone is not a significant etiologic contributor, and calls for functional validation. Machine propagation converts this weak, interaction-dependent association into a normal-development process assertion that is too strong for current evidence. Propagation Review Root cause: SOURCE WEAK OR INFERRED Failure modes: SOURCE EVIDENCE WEAK CONTEXT OR TISSUE MISMATCH Sources checked: ARBA:ARBA00091405 · ARBA face-morphogenesis model SOURCE WEAK OR INFERRED The source relationship is an association and expression-based inference, not a CRISPLD1 mutant/rescue demonstration of face morphogenesis. Supporting Evidence: PMID:21254358 We show that only one CRISPLD1 SNP, rs1455809, had marginally altered transmission (p=0.05) suggesting that variation in CRISPLD1 alone does not play a significant etiologic role in NSCLP. |
| GO:0070062 extracellular exosome | HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... | MARK AS OVER ANNOTATED | Summary: Detected in an extracellular-vesicle proteome, but the detection does not establish that this protein is an EV constituent. Reason: Secreted protein. Secreted or lumenal protein (UniProt). MISEV2018 (PMID:30637094) category 5 allows such proteins onto EVs through specific or promiscuous (proteoglycan, lipid) receptors on the EV surface, but asks that their identification be backed by evidence of that association. A bulk EV proteome cannot separate surface binding from co-isolation, and this protein's annotations record no experimental proteoglycan, heparin or lipid binding, and its own review keeps no experimental cell-surface or plasma-membrane pool. (Manual re-review for OMICS_EVIDENCE, 2026-10-10; previous action: KEEP_AS_NON_CORE.) Supporting Evidence: PMID:23533145 in total, close to 900 proteins were identified in the two EPS-urine exosome pools PMID:23533145 some of these proteins could also exist as a soluble form. |
| GO:0060325 face morphogenesis | IMP PMID:21254358 Nonsyndromic cleft lip and palate: CRISPLD genes and the fol... | MARK AS OVER ANNOTATED | Summary: This annotation treats the cleft-lip/palate family-association study as mutant phenotype evidence for face morphogenesis. Reason: Full-text review does not reveal a CRISPLD1 perturbation or rescue experiment. The study found no significant CRISPLD1-alone etiologic effect and instead reported marginal transmission and statistical interactions among CRISPLD1, CRISPLD2, and folate-pathway variants. Developmental expression and association make the process plausible, so this is marked over-annotated rather than declared biologically impossible, but it should not define CRISPLD1's core function. Supporting Evidence: PMID:21254358 We show that only one CRISPLD1 SNP, rs1455809, had marginally altered transmission (p=0.05) suggesting that variation in CRISPLD1 alone does not play a significant etiologic role in NSCLP. PMID:21254358 These results are intriguing and require both validation and functional studies |
| GO:0070062 extracellular exosome | HDA PMID:19199708 Proteomic analysis of human parotid gland exosomes by multid... | MARK AS OVER ANNOTATED | Summary: Detected in an extracellular-vesicle proteome, but the detection does not establish that this protein is an EV constituent. Reason: Secreted protein. Secreted or lumenal protein (UniProt). MISEV2018 (PMID:30637094) category 5 allows such proteins onto EVs through specific or promiscuous (proteoglycan, lipid) receptors on the EV surface, but asks that their identification be backed by evidence of that association. A bulk EV proteome cannot separate surface binding from co-isolation, and this protein's annotations record no experimental proteoglycan, heparin or lipid binding, and its own review keeps no experimental cell-surface or plasma-membrane pool. (Manual re-review for OMICS_EVIDENCE, 2026-10-10; previous action: KEEP_AS_NON_CORE.) Supporting Evidence: PMID:19199708 Using MudPIT (multidimensional protein identification technology) mass spectrometry, we catalogued 491 proteins in the exosome fraction of human parotid saliva. PMID:19199708 Alternatively, some minor contamination may have occurred during the isolation procedure of the exosomes. |
| GO:0051481 negative regulation of cytosolic calcium ion concentration | IMP PMID:32146539 CRISPLD1: a novel conserved target in the transition to huma... | NEW | Summary: CRISPR/Cas9 loss of CRISPLD1 in human iPSC-derived cardiomyocytes increased calcium-transient amplitude and changed rise and decay kinetics, producing higher systolic calcium transients. Reason: The direction of the loss-of-function phenotype supports normal CRISPLD1 as a negative regulator of cytosolic calcium transients in cardiomyocytes, and the authors explicitly interpret the combined loss-of-function/rescue results as an inhibitory role in calcium cycling. This process annotation does not presume a direct calcium-channel target, which remains untested. Supporting Evidence: PMID:32146539 pointing towards higher systolic CaT in KO-CM. PMID:32146539 This loss-of-function and rescue experiments support the converse argument, that CRISPLD1 plays an inhibitory role in CM Ca2+ cycling. file:human/CRISPLD1/CRISPLD1-deep-research-manual.md Current evidence establishes secretion and regulation of cardiomyocyte calcium transients but does not establish a direct calcium-channel or adaptor activity. |
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Download this section (compressed HTML)Q: Which extracellular receptor or calcium-handling protein mediates the CRISPLD1 effect on cardiomyocyte calcium transients?
Q: Are the CAP domain, either LCCL domain, and secretion individually required for the calcium-cycling phenotype?
Q: Does CRISPLD1 have a direct developmental role in craniofacial morphogenesis, or do the reported human associations reflect linkage and multigene folate-pathway context?
Experiment: Produce correctly folded, glycosylated CRISPLD1 and apply it acutely to wild-type and CRISPLD1-knockout iPSC-derived cardiomyocytes. Measure calcium transients, sarcoplasmic-reticulum calcium load, action potentials, and RyR2/L-type-calcium-channel currents; test neutralizing antibodies and washout to distinguish acute extracellular signaling from long-term transcriptional adaptation.
Hypothesis: Secreted CRISPLD1 directly inhibits a cardiomyocyte calcium-handling protein.
Type: Protein add-back with calcium imaging and electrophysiology
Experiment: Rescue isogenic CRISPLD1-knockout cardiomyocytes with wild-type protein, a signal-peptide mutant, CAP-domain mutants, and individual LCCL-domain deletions at matched expression. Quantify secretion, folding, calcium-transient parameters, and recovery of the knockout transcriptomic signature.
Hypothesis: CRISPLD1's CAP and LCCL domains make distinct contributions to secretion and calcium regulation.
Type: Domain-resolved knockout rescue
Experiment: Introduce CRISPLD1 risk alleles or null alleles alone and in combination with CRISPLD2/folate-pathway variants into human cranial-neural-crest organoid models. Measure migration, survival, facial-mesenchyme differentiation, matrix organization, and rescue by wild-type CRISPLD1 under controlled folate conditions.
Hypothesis: CRISPLD1 contributes directly to craniofacial morphogenesis only in combination with specific CRISPLD2 or folate-pathway genotypes.
Type: Combinatorial isogenic craniofacial-development model
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: CRISPLD1's direct molecular activity, extracellular target/receptor, calcium-handling effector, and activity-bearing domain are unknown.
OPEN BIOLOGY MF_DARK
What is known: Human cardiomyocyte loss of function establishes regulation of calcium-transient amplitude and kinetics, but no experiment has shown direct channel binding, channel-current modulation, adaptor activity, or catalysis by purified CRISPLD1.
Significance: Resolving this mechanism is required before assigning calcium channel regulator or another specific molecular-function term and is essential for interpreting the increase of CRISPLD1 during pressure-overload heart failure.
What would resolve it: Test purified/full-length CRISPLD1 and domain variants against candidate cardiac calcium-handling proteins, measure channel currents and calcium flux, and perform knockout rescue with secretion-defective and domain-deletion constructs.
Provenance (the field's own admissions):
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