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... | KEEP AS NON CORE | Summary: CRISPLD1 was identified by shotgun proteomics in exosome-enriched expressed prostatic secretions in urine. Reason: The HDA observation is retained as context-specific localization evidence and is consistent with CRISPLD1 secretion. It does not establish that CRISPLD1 is a constitutive exosome component or functions on/in vesicles: the study used a high-complexity ultracentrifugation preparation and explicitly notes that some proteins may also occur in soluble form. 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... | KEEP AS NON CORE | Summary: CRISPLD1 was identified by MudPIT in an exosome-enriched fraction of human parotid saliva. Reason: This independent extracellular-fluid proteome corroborates secretion and supports retaining the HDA observation. It remains non-core because the study does not establish CRISPLD1's vesicle topology or function and explicitly acknowledges that abundant secreted proteins can be incorporated during vesicle formation or arise from minor preparation contamination. 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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