CAPN8

calpain 8, the group of Calpains|EF-hand domain containing

Basic information

Region (hg38): 1:223538007-223665723

Links

ENSG00000203697 ∙ NCBI:388743 ∙ OMIM:618777 ∙ HGNC:1485 ∙ Uniprot:A6NHC0 ∙ 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 CAPN8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN8 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				1		1
missense			27	3		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	27	4	0

Variants in CAPN8

This is a list of pathogenic ClinVar variants found in the CAPN8 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-223612249-C-T			Likely benign (May 01, 2022)
1-223616112-C-T		not specified	Likely benign (Aug 09, 2021)
1-223616136-C-G		not specified	Uncertain significance (Sep 17, 2021)
1-223619299-A-G		not specified	Uncertain significance (Oct 22, 2024)
1-223619319-G-A		not specified	Uncertain significance (Apr 06, 2023)
1-223619328-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-223619329-G-A		not specified	Uncertain significance (Jul 02, 2024)
1-223619340-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-223619360-C-A		not specified	Uncertain significance (Dec 14, 2022)
1-223619403-T-G		not specified	Uncertain significance (Nov 08, 2022)
1-223619407-A-G		not specified	Uncertain significance (Aug 28, 2024)
1-223619409-A-T		not specified	Uncertain significance (Aug 13, 2021)
1-223619410-T-A		not specified	Uncertain significance (Jan 26, 2022)
1-223619418-C-T		not specified	Uncertain significance (Aug 10, 2024)
1-223619446-G-C		not specified	Uncertain significance (Dec 09, 2023)
1-223620222-A-G		not specified	Uncertain significance (May 15, 2023)
1-223620237-C-T		not specified	Likely benign (Jul 09, 2021)
1-223620238-G-A		not specified	Uncertain significance (Jan 10, 2023)
1-223620246-A-G		not specified	Uncertain significance (Apr 24, 2024)
1-223622828-C-A		not specified	Uncertain significance (Dec 21, 2022)
1-223625876-C-A		not specified	Uncertain significance (Nov 19, 2022)
1-223625878-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-223625888-C-T		not specified	Uncertain significance (Apr 15, 2024)
1-223627033-G-A		not specified	Uncertain significance (Sep 04, 2024)
1-223627045-A-G		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN8	protein_coding	protein_coding	ENST00000366872	20	142088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.25e-13	0.491	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.844	342	389	0.879	0.0000222	4425
Missense in Polyphen		60	79.166	0.7579		860
Synonymous	1.31	137	158	0.867	0.0000100	1297
Loss of Function	1.46	25	34.2	0.730	0.00000146	411

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. Involved in membrane trafficking in the gastric surface mucus cells (pit cells) and may involve the membrane trafficking of mucus cells via interactions with coat protein. Proteolytically cleaves the beta- subunit of coatomer complex (By similarity). {ECO:0000250}.
• Pathway: Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Haploinsufficiency Scores

• pHI: 0.0658
• hipred: N
• hipred_score: 0.220

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0834

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn8
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

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