CAPN13

protein-coding

calpain 13, the group of Calpains

Gene summary

The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes a member of the calpain large subunit family. [provided by RefSeq, Jun 2012]

MANE transcript

NM_144575.3

Inheritance

—

ClinVar variants

U:123B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr2:30,722,771-30,820,542

External References & Databases

Ensembl (ENSG00000162949)

Transcript & Mutation Effects

hg38 • Region Span ~97.8 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 CAPN13 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 129

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144575.3. 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	1 clinvar		2
missense			117 clinvar	11 clinvar		128
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	123	12	0	135

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144575.3	RefSeq	NP_653176.2	21	MANE Select
ENST00000295055.12	Ensembl	ENSP00000295055.8	21	MANE Select
ENST00000450650.5	Ensembl	ENSP00000403180.1	5	Standard
ENST00000458085.6	Ensembl	ENSP00000416191.2	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Extracellular matrix organization
Degradation of the extracellular matrix

Biological Process

proteolysis

Molecular Function

calcium-dependent cysteine-type endopeptidase activity
calcium ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295055
Coding exons: 21
Length: 97772
Individuals with no LoFs: 124311
Homozygous LoFs: 0
Heterozygous LoFs: 355
Defined: 124666
p: 0.00142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0870	389	384	1.01	0.0000226	4388
Missense (PolyPhen)		113	110.45	1.0231		1467
Synonymous	-0.939	156	142	1.10	0.00000822	1229
Loss of Function	0.879	37	43.2	0.856	0.00000209	476

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00095	0.00084	rare
Latino/Admixed American	0.0018	0.0017	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0076	0.0075	notable
Finnish	0.00094	0.00093	rare
European (Non-Finnish)	0.00088	0.00086	rare
South Asian	0.00073	0.00072	rare
Other	0.0012	0.0012	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable non-lysosomal thiol-protease. {ECO:0000250}.;

Recessive Scores

pRec: 0.0780

Intolerance Scores

LoFtool: 0.364
RVIS EVS: -0.28
RVIS percentile EVS: 33.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.303

Gene Damage Prediction

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