CAPN6

calpain 6, the group of Calpains|C2 domain containing

Basic information

Region (hg38): X:111245099-111270483

Links

ENSG00000077274 ∙ NCBI:827 ∙ OMIM:300146 ∙ HGNC:1483 ∙ Uniprot:Q9Y6Q1 ∙ 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 CAPN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN6 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	2	3
missense			14		1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					9	9
Total	0	0	14	1	12

Variants in CAPN6

This is a list of pathogenic ClinVar variants found in the CAPN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-111246658-C-G		not specified	Uncertain significance (Nov 07, 2022)
X-111246746-C-T		Malignant tumor of prostate	Uncertain significance (-)
X-111247114-G-A			Benign (Jun 21, 2021)
X-111247263-C-T			Benign (Jun 19, 2021)
X-111247922-G-C		not specified	Uncertain significance (Oct 26, 2022)
X-111247935-C-T			Likely benign (Mar 01, 2023)
X-111247953-G-T		not specified	Uncertain significance (Oct 29, 2024)
X-111248579-C-G		not specified	Uncertain significance (Mar 28, 2024)
X-111248614-C-G		not specified	Uncertain significance (Nov 09, 2022)
X-111248637-G-A			Benign (Nov 14, 2017)
X-111248676-G-C		not specified	Uncertain significance (Apr 25, 2023)
X-111248701-A-G		not specified	Uncertain significance (Dec 26, 2023)
X-111248713-G-A		not specified	Uncertain significance (Oct 04, 2022)
X-111248713-G-T		not specified	Uncertain significance (Jun 11, 2024)
X-111248754-T-G		not specified	Uncertain significance (Apr 07, 2023)
X-111248960-T-C		not specified	Uncertain significance (Jul 07, 2022)
X-111248994-G-A		not specified	Uncertain significance (Oct 04, 2024)
X-111250789-T-A			Benign (Jun 19, 2021)
X-111251053-C-T		not specified	Uncertain significance (Feb 14, 2023)
X-111251300-GA-G			Benign (Jun 18, 2021)
X-111251300-G-GA			Benign (Jun 18, 2021)
X-111251613-C-G			Benign (Jun 09, 2021)
X-111251625-T-C		not specified	Uncertain significance (Jul 17, 2024)
X-111251664-G-A		not specified	Uncertain significance (Nov 12, 2024)
X-111251724-G-T		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN6	protein_coding	protein_coding	ENST00000324068	12	25421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.819	0.181	125732	3	7	125742	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	187	255	0.733	0.0000199	4254
Missense in Polyphen		67	110.49	0.6064		1647
Synonymous	-0.991	97	85.4	1.14	0.00000593	1195
Loss of Function	3.70	4	23.2	0.172	0.00000176	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000136	0.0000992
East Asian	0.00	0.00
Finnish	0.000129	0.0000924
European (Non-Finnish)	0.0000858	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-stabilizing protein that may be involved in the regulation of microtubule dynamics and cytoskeletal organization. May act as a regulator of RAC1 activity through interaction with ARHGEF2 to control lamellipodial formation and cell mobility. Does not seem to have protease activity as it has lost the active site residues (By similarity). {ECO:0000250, ECO:0000269|PubMed:17210638}.
• Pathway: Integrin-mediated Cell Adhesion;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.138
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.636
• hipred: Y
• hipred_score: 0.707
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn6
• Phenotype: muscle phenotype; craniofacial phenotype; growth/size/body region phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: microtubule bundle formation;proteolysis;regulation of cytoskeleton organization
• Cellular component: cytoplasm;cytosol;spindle microtubule;perinuclear region of cytoplasm
• Molecular function: calcium-dependent cysteine-type endopeptidase activity;microtubule binding