CAPN14

calpain 14, the group of Calpains|EF-hand domain containing

Basic information

Region (hg38): 2:31173056-31233858

Links

ENSG00000214711 ∙ NCBI:440854 ∙ OMIM:610229 ∙ HGNC:16664 ∙ Uniprot:A8MX76 ∙ 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 CAPN14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN14 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			52	3		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	3	1

Variants in CAPN14

This is a list of pathogenic ClinVar variants found in the CAPN14 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-31174698-T-C		not specified	Uncertain significance (Jun 06, 2023)
2-31174704-T-C		not specified	Uncertain significance (Dec 27, 2023)
2-31176605-T-C		not specified	Uncertain significance (Oct 26, 2022)
2-31176615-C-A		not specified	Uncertain significance (Feb 26, 2024)
2-31177032-T-C		not specified	Uncertain significance (Dec 19, 2023)
2-31177048-C-A		not specified	Uncertain significance (Feb 14, 2024)
2-31177050-T-C		not specified	Uncertain significance (May 04, 2023)
2-31177052-A-C		not specified	Uncertain significance (Jun 10, 2024)
2-31177058-A-T		not specified	Uncertain significance (Nov 12, 2021)
2-31177095-C-T		not specified	Uncertain significance (May 12, 2024)
2-31177100-C-A		not specified	Uncertain significance (Mar 07, 2023)
2-31177766-T-C		not specified	Likely benign (Jan 23, 2024)
2-31177767-G-A		not specified	Uncertain significance (Aug 04, 2021)
2-31177800-G-C		not specified	Uncertain significance (Nov 18, 2022)
2-31178546-A-G		not specified	Uncertain significance (Jul 15, 2021)
2-31187775-T-A		not specified	Uncertain significance (Jul 09, 2021)
2-31187813-T-A		not specified	Uncertain significance (Dec 06, 2022)
2-31188329-C-T		not specified	Uncertain significance (Sep 22, 2023)
2-31189343-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-31189448-C-T		not specified	Uncertain significance (Apr 12, 2022)
2-31191964-G-A		Amyotrophic lateral sclerosis	Conflicting classifications of pathogenicity (Sep 09, 2020)
2-31191967-G-T		not specified	Uncertain significance (Dec 16, 2023)
2-31191979-G-A		not specified	Uncertain significance (Sep 26, 2022)
2-31192012-C-T		not specified	Uncertain significance (Nov 22, 2023)
2-31192045-C-A		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN14	protein_coding	protein_coding	ENST00000403897	21	60801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-21	0.0192	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	299	359	0.832	0.0000195	4480
Missense in Polyphen		101	121.48	0.83141		1635
Synonymous	1.36	124	145	0.856	0.00000813	1269
Loss of Function	0.959	36	42.8	0.842	0.00000201	497

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. {ECO:0000250}.
• Pathway: Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Intolerance Scores

• rvis_EVS: 2.66
• rvis_percentile_EVS: 98.84

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0977

Gene Damage Prediction

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

Gene ontology

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