CAPN11

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

Basic information

Region (hg38): 6:44158811-44184401

Links

ENSG00000137225 ∙ NCBI:11131 ∙ OMIM:604822 ∙ HGNC:1478 ∙ Uniprot:Q9UMQ6 ∙ 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 CAPN11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN11 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					2	2
missense			34	4		38
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	5	2

Variants in CAPN11

This is a list of pathogenic ClinVar variants found in the CAPN11 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44158854-G-A			Benign (Oct 30, 2018)
6-44166815-G-C		not specified	Uncertain significance (Jun 26, 2023)
6-44166826-G-C		not specified	Uncertain significance (Mar 25, 2024)
6-44169299-C-T		not specified	Uncertain significance (Aug 26, 2022)
6-44169328-C-T		not specified	Uncertain significance (Dec 07, 2021)
6-44169329-G-A		not specified	Uncertain significance (Apr 24, 2023)
6-44169350-G-A		not specified	Uncertain significance (Apr 08, 2024)
6-44169358-G-A		not specified	Uncertain significance (Oct 26, 2022)
6-44169475-A-G		not specified	Uncertain significance (Dec 20, 2022)
6-44169936-G-A		not specified	Likely benign (Jul 12, 2023)
6-44169958-T-C		not specified	Uncertain significance (Apr 01, 2024)
6-44169963-C-T			Likely benign (Dec 31, 2019)
6-44172340-A-T		not specified	Uncertain significance (Nov 21, 2023)
6-44172345-C-T			Benign (Jul 15, 2018)
6-44172362-G-A		not specified	Uncertain significance (Feb 03, 2022)
6-44172364-G-A		not specified	Uncertain significance (Apr 19, 2024)
6-44172365-T-G		not specified	Uncertain significance (Apr 26, 2023)
6-44172390-G-C		not specified	Uncertain significance (Dec 12, 2023)
6-44172406-A-G		not specified	Uncertain significance (Jan 29, 2024)
6-44173226-G-A		not specified	Uncertain significance (May 24, 2024)
6-44173264-G-A		not specified	Uncertain significance (May 09, 2022)
6-44173273-G-A		not specified	Uncertain significance (Sep 25, 2023)
6-44173288-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-44173373-G-C		not specified	Uncertain significance (Feb 05, 2024)
6-44176305-G-A		not specified	Uncertain significance (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN11	protein_coding	protein_coding	ENST00000398776	23	25592

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.41e-24	0.00434	123973	2	781	124756	0.00314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.233	399	412	0.968	0.0000225	4895
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0116	0.0115
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.00577	0.00563
Finnish	0.0104	0.00965
European (Non-Finnish)	0.00209	0.00202
Middle Eastern	0.00577	0.00563
South Asian	0.00105	0.00105
Other	0.00202	0.00198

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction.
• Pathway: Integrin-mediated Cell Adhesion;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.0890

Intolerance Scores

• loftool: 0.337
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.24

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.153
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00721

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn11
• Phenotype: normal phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

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