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.

not_specified (39 variants)
not_provided (3 variants)
Prostate_cancer (1 variants)
Neurodevelopmental_delay (1 variants)

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. These statistics are base on transcript: NM_000014289.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	2 clinvar	3
missense			40 clinvar			40
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	1	0	40	1	2

Highest pathogenic variant AF is 0.0000018216446

Loading clinvar variants...

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