CAPN11

protein-coding

calpain 11, the group of Calpains|EF-hand domain containing

Gene summary

Calpains constitute a family of intracellular calcium-dependent cysteine proteases. There are eight members in this superfamily. They consist of a variable 80 kDa subunit and an invariant 30 kDa subunit. This calpain protein appears to have protease activity and calcium-binding ability. A similar mouse protein may play a functional role in spermatogenesis and in the regulation of calcium-dependent signal transduction events during meiosis. [provided by RefSeq, Dec 2008]

MANE transcript

NM_007058.4

Inheritance

—

ClinVar variants

U:103B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr6:44,158,811-44,184,401

External References & Databases

Ensembl (ENSG00000137225)

Transcript & Mutation Effects

hg38 • Region Span ~25.6 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 CAPN11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 104

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007058.4. 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			1 clinvar		2 clinvar	3
missense			100 clinvar	6 clinvar		106
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	103	7	2	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007058.4	RefSeq	NP_008989.2	23	MANE Select
ENST00000398776.2	Ensembl	ENSP00000381758.1	23	MANE Select
ENST00000526118.1	Ensembl	ENSP00000431963.1	2	Standard
ENST00000532171.5	Ensembl	ENSP00000432420.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Integrin-mediated Cell Adhesion
Extracellular matrix organization
Degradation of the extracellular matrix

Biological Process

proteolysis

Molecular Function

calcium-dependent cysteine-type endopeptidase activity
calcium ion binding
peptidase activity

Cellular Component

acrosomal vesicle
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398776
Coding exons: 23
Length: 25592
Individuals with no LoFs: 123973
Homozygous LoFs: 2
Heterozygous LoFs: 781
Defined: 124756
p: 0.00314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.233	399	412	0.968	0.0000225	4895
Missense (PolyPhen)		142	149.47	0.95		1697
Synonymous	0.0209	160	160	0.998	0.00000923	1330
Loss of Function	0.734	39	44.3	0.881	0.00000206	516

Population LoF Frequency

Population	CAF	p-value	Status
African	0.010	0.010	notable
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0058	0.0056	notable
Finnish	0.010	0.0097	notable
European (Non-Finnish)	0.0021	0.0020	notable
South Asian	0.0011	0.0010	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction.;

Recessive Scores

pRec: 0.0890

Intolerance Scores

LoFtool: 0.337
RVIS EVS: 0.78
RVIS percentile EVS: 87.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00721

Gene Damage Prediction

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