CAPN13

calpain 13, the group of Calpains

Basic information

Region (hg38): 2:30722770-30820542

Links

ENSG00000162949 ∙ NCBI:92291 ∙ OMIM:610228 ∙ HGNC:16663 ∙ Uniprot:Q6MZZ7 ∙ 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 CAPN13 gene.

• Inborn genetic diseases (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN13 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			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in CAPN13

This is a list of pathogenic ClinVar variants found in the CAPN13 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-30731348-A-G		not specified	Uncertain significance (Jun 23, 2021)
2-30731360-T-G		not specified	Uncertain significance (Jun 18, 2021)
2-30731388-T-C		not specified	Uncertain significance (Jan 30, 2024)
2-30731392-G-T		not specified	Uncertain significance (Jan 04, 2022)
2-30732475-G-C		not specified	Uncertain significance (Dec 06, 2023)
2-30732495-C-T		not specified	Uncertain significance (Sep 27, 2021)
2-30732510-A-G		not specified	Uncertain significance (Nov 21, 2022)
2-30732562-G-T		not specified	Uncertain significance (Mar 17, 2023)
2-30734478-G-A		not specified	Uncertain significance (Dec 11, 2023)
2-30734523-T-G		not specified	Uncertain significance (Nov 09, 2021)
2-30736519-C-T		not specified	Uncertain significance (Jun 10, 2022)
2-30736534-G-A		not specified	Uncertain significance (Dec 13, 2023)
2-30738439-T-G		not specified	Uncertain significance (Jul 14, 2022)
2-30741916-C-G		not specified	Uncertain significance (Sep 25, 2023)
2-30742333-C-A		not specified	Uncertain significance (Mar 16, 2022)
2-30742348-C-T		not specified	Uncertain significance (Oct 25, 2023)
2-30743389-C-G		not specified	Uncertain significance (Apr 13, 2022)
2-30743449-G-C		not specified	Uncertain significance (Apr 06, 2022)
2-30743521-C-A		not specified	Uncertain significance (Jan 10, 2023)
2-30743542-G-A		not specified	Uncertain significance (Jul 06, 2021)
2-30743552-A-G		not specified	Uncertain significance (Sep 06, 2022)
2-30743561-G-T		not specified	Uncertain significance (Dec 12, 2023)
2-30751120-C-T		not specified	Likely benign (Sep 25, 2023)
2-30751183-C-T		not specified	Uncertain significance (Mar 01, 2024)
2-30751191-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN13	protein_coding	protein_coding	ENST00000295055	21	97772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.15e-22	0.0115	124311	0	355	124666	0.00142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0870	389	384	1.01	0.0000226	4388
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00272	0.00262
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.00757	0.00748
Finnish	0.000939	0.000929
European (Non-Finnish)	0.000879	0.000858
Middle Eastern	0.00757	0.00748
South Asian	0.000726	0.000719
Other	0.00118	0.00116

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable non-lysosomal thiol-protease. {ECO:0000250}.
• Pathway: Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.0780

Intolerance Scores

• loftool: 0.364
• rvis_EVS: -0.28
• rvis_percentile_EVS: 33.56

Haploinsufficiency Scores

• pHI: 0.0607
• hipred: N
• hipred_score: 0.145
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.303

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn13

Gene ontology

• Biological process: proteolysis
• Cellular component: cytoplasm
• Molecular function: calcium-dependent cysteine-type endopeptidase activity;calcium ion binding