CAPNS2

calpain small subunit 2, the group of EF-hand domain containing

Basic information

Region (hg38): 16:55566683-55567687

Links

ENSG00000256812 ∙ NCBI:84290 ∙ OMIM:616767 ∙ HGNC:16371 ∙ Uniprot:Q96L46 ∙ 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 CAPNS2 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPNS2 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in CAPNS2

This is a list of pathogenic ClinVar variants found in the CAPNS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-55566760-T-A		not specified	Uncertain significance (Jun 23, 2023)
16-55566784-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-55566797-G-A		not specified	Uncertain significance (Dec 07, 2021)
16-55566809-C-T		not specified	Uncertain significance (Dec 12, 2023)
16-55566926-C-G		not specified	Uncertain significance (Feb 28, 2023)
16-55566926-C-T		not specified	Uncertain significance (Aug 20, 2023)
16-55566934-C-T		not specified	Uncertain significance (Dec 19, 2023)
16-55566985-G-C		not specified	Uncertain significance (Nov 22, 2023)
16-55567130-G-A		not specified	Uncertain significance (Oct 18, 2021)
16-55567153-A-G		not specified	Uncertain significance (May 30, 2023)
16-55567209-C-G		not specified	Uncertain significance (Jul 21, 2021)
16-55567303-T-G		not specified	Uncertain significance (Dec 19, 2023)
16-55567448-A-T		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPNS2	protein_coding	protein_coding	ENST00000457326	1	1016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00193	0.747	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0812	134	137	0.980	0.00000747	1626
Missense in Polyphen		47	41.107	1.1434		479
Synonymous	0.637	44	49.7	0.885	0.00000250	498
Loss of Function	0.893	5	7.67	0.652	4.79e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction. This small subunit may act as a tissue-specific chaperone of the large subunit, possibly by helping it fold into its correct conformation for activity.
• Pathway: Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer,s disease models;Neurodegenerative Diseases;Disease;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Intolerance Scores

• loftool: 0.658
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.34

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capns2

Gene ontology

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