CAPN10

calpain 10, the group of Calpains

Basic information

Region (hg38): 2:240586734-240617705

Links

ENSG00000142330 ∙ NCBI:11132 ∙ OMIM:605286 ∙ HGNC:1477 ∙ Uniprot:Q9HC96 ∙ 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 CAPN10 gene.

• CAPN10-related disorder (1 variants)
• not provided (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN10 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				15	3	18
missense			49	10	6	65
nonsense						0
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region					3	3
non coding				1		1
Total	3	0	49	26	9

Variants in CAPN10

This is a list of pathogenic ClinVar variants found in the CAPN10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-240586919-C-T		Inborn genetic diseases	Uncertain significance (Mar 31, 2024)
2-240586936-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
2-240586953-C-G		Inborn genetic diseases	Uncertain significance (May 02, 2024)
2-240587011-C-G			Benign (Dec 31, 2019)
2-240587036-C-T		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
2-240587047-C-T		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
2-240589349-T-C		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
2-240589388-G-A		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
2-240589439-G-A		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
2-240589444-G-A			Likely benign (Jun 10, 2018)
2-240590834-C-T		Inborn genetic diseases	Uncertain significance (Sep 21, 2023)
2-240590894-G-A		Inborn genetic diseases	Likely benign (Sep 20, 2023)
2-240590920-C-T			Uncertain significance (Apr 09, 2022)
2-240590956-C-T		Inborn genetic diseases	Uncertain significance (Apr 21, 2022)
2-240590957-G-A		Inborn genetic diseases	Uncertain significance (Feb 02, 2024)
2-240590970-G-C		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)
2-240591000-G-A		CAPN10-related disorder	Likely benign (May 28, 2019)
2-240591006-C-T			Likely benign (Dec 31, 2019)
2-240591007-G-A		Inborn genetic diseases	Uncertain significance (Mar 18, 2019)
2-240591746-T-C		• Type 2 diabetes mellitus 1, susceptibility to	risk factor (Nov 01, 2003)
2-240591757-G-A		Type 2 diabetes mellitus 1, susceptibility to	risk factor (Jul 01, 2004)
2-240591938-A-G		Inborn genetic diseases	Uncertain significance (Oct 03, 2023)
2-240591948-C-T			Likely benign (Jun 10, 2018)
2-240592060-C-A			Benign (Dec 31, 2019)
2-240592062-A-G		CAPN10-related disorder	Benign (Oct 17, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN10	protein_coding	protein_coding	ENST00000391984	12	30990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.92e-13	0.620	125671	0	76	125747	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	357	425	0.841	0.0000282	4261
Missense in Polyphen		123	152.26	0.80784		1682
Synonymous	-0.697	207	195	1.06	0.0000137	1426
Loss of Function	1.56	24	33.8	0.710	0.00000163	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000479	0.000476
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.000791	0.000786
European (Non-Finnish)	0.000288	0.000273
Middle Eastern	0.000329	0.000326
South Asian	0.000169	0.000163
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction. May play a role in insulin-stimulated glucose uptake. {ECO:0000269|PubMed:17572128}.
• Pathway: Integrin-mediated Cell Adhesion;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.211

Intolerance Scores

• loftool: 0.111
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.92

Haploinsufficiency Scores

• pHI: 0.0693
• hipred: N
• hipred_score: 0.379
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn10
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; renal/urinary system phenotype; immune system phenotype

Gene ontology

• Biological process: proteolysis;cellular component disassembly involved in execution phase of apoptosis;actin cytoskeleton reorganization;positive regulation of insulin secretion;positive regulation of intracellular transport;cellular response to insulin stimulus;positive regulation of glucose import;type B pancreatic cell apoptotic process;positive regulation of type B pancreatic cell apoptotic process
• Cellular component: cytoplasm;mitochondrion;cytosol;plasma membrane
• Molecular function: SNARE binding;calcium-dependent cysteine-type endopeptidase activity;cytoskeletal protein binding