CAPN7

calpain 7, the group of Calpains

Basic information

Region (hg38): 3:15206152-15252916

Links

ENSG00000131375 ∙ NCBI:23473 ∙ OMIM:606400 ∙ HGNC:1484 ∙ Uniprot:Q9Y6W3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAPN7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			47	3		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	48	3	0

Variants in CAPN7

This is a list of pathogenic ClinVar variants found in the CAPN7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-15206514-G-C		not specified	Uncertain significance (Aug 06, 2021)
3-15206523-G-T		not specified	Uncertain significance (Dec 30, 2024)
3-15206524-C-A		not specified	Uncertain significance (Dec 30, 2024)
3-15206530-A-G		not specified	Uncertain significance (Jan 23, 2024)
3-15206575-C-G		not specified	Uncertain significance (Nov 26, 2024)
3-15206581-C-T		not specified	Uncertain significance (Apr 01, 2024)
3-15212110-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-15212117-C-A		not specified	Uncertain significance (Nov 18, 2022)
3-15212180-A-T		not specified	Uncertain significance (Jan 21, 2025)
3-15212182-C-G		not specified	Uncertain significance (Jul 05, 2023)
3-15212189-G-C		not specified	Uncertain significance (Feb 28, 2023)
3-15217433-A-C		not specified	Uncertain significance (Feb 15, 2023)
3-15217443-A-G		not specified	Uncertain significance (Oct 26, 2021)
3-15217476-A-G		not specified	Uncertain significance (Aug 08, 2023)
3-15217478-C-G		not specified	Uncertain significance (Mar 10, 2025)
3-15217512-A-C		not specified	Uncertain significance (Apr 20, 2024)
3-15217541-A-G			Likely benign (Apr 01, 2023)
3-15217542-T-C		not specified	Uncertain significance (Nov 10, 2024)
3-15218476-T-C		not specified	Uncertain significance (Oct 06, 2022)
3-15218525-G-C		not specified	Uncertain significance (Jun 24, 2022)
3-15220789-C-T		not specified	Uncertain significance (Jan 08, 2025)
3-15220829-T-G		not specified	Likely benign (Dec 11, 2024)
3-15220836-A-G		not specified	Uncertain significance (Jun 11, 2021)
3-15220923-C-T		not specified	Uncertain significance (Jul 25, 2024)
3-15220942-A-G		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN7	protein_coding	protein_coding	ENST00000253693	21	46767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-13	0.995	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	347	417	0.833	0.0000202	5312
Missense in Polyphen		92	144.28	0.63764		1805
Synonymous	-0.903	155	141	1.10	0.00000683	1476
Loss of Function	2.76	29	50.1	0.579	0.00000266	614

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000812	0.000811
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000497	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000413	0.000396
Middle Eastern	0.000497	0.000489
South Asian	0.000265	0.000261
Other	0.000334	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-regulated non-lysosomal thiol-protease. {ECO:0000250}.
• Pathway: Integrin-mediated Cell Adhesion;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.335
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.7

Haploinsufficiency Scores

• pHI: 0.0993
• hipred: N
• hipred_score: 0.414
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.467

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn7
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of epithelial cell migration;self proteolysis
• Cellular component: nucleus;extracellular exosome
• Molecular function: endopeptidase activity;calcium-dependent cysteine-type endopeptidase activity;protein binding;MIT domain binding