CAPSL

protein-coding

calcyphosine like, the group of EF-hand domain containing

Gene summary

Predicted to enable calcium ion binding activity. Predicted to act upstream of or within several processes, including blood vessel morphogenesis; endothelial cell migration; and endothelial cell proliferation. Predicted to be located in cytoplasm and organelle. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001042625.2

Inheritance

—

ClinVar variants

U:41B:1

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr5:35,904,288-35,938,779

External References & Databases

Ensembl (ENSG00000152611)

Transcript & Mutation Effects

hg38 • Region Span ~34.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CAPSL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 2

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042625.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			39 clinvar		1 clinvar	40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	41	0	1	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042625.2	RefSeq	NP_001036090.1	4	MANE Select
ENST00000651391.1	Ensembl	ENSP00000498465.1	4	MANE Select
NM_144647.4	RefSeq	NP_653248.3	4	Standard
ENST00000397366.5	Ensembl	ENSP00000380523.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397367
Coding exons: 4
Length: 34485
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125748
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.491	134	119	1.13	0.00000625	1387
Missense (PolyPhen)		50	35.528	1.4074		441
Synonymous	-1.43	55	43.1	1.28	0.00000248	367
Loss of Function	-0.0126	10	9.96	1.00	6.56e-7	112

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.0010	0.00098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.470
RVIS EVS: -0.09
RVIS percentile EVS: 46.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium