COL6A6

collagen type VI alpha 6 chain, the group of Collagens

Basic information

Region (hg38): 3:130517177-130677044

Links

ENSG00000206384 ∙ NCBI:131873 ∙ OMIM:616613 ∙ HGNC:27023 ∙ Uniprot:A6NMZ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopathy (Limited), mode of inheritance: AR
• congenital myopathy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COL6A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL6A6 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				8	9	17
missense			203	18	11	232
nonsense			1			1
start loss						0
frameshift			1	1		2
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1	1		3
splice region				1	2	3
non coding				1		1
Total	0	1	206	29	20

Variants in COL6A6

This is a list of pathogenic ClinVar variants found in the COL6A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-130560389-G-C		not specified	Uncertain significance (Feb 13, 2025)
3-130560405-A-T		not specified	Uncertain significance (Oct 20, 2021)
3-130560427-C-T			Benign (Dec 31, 2019)
3-130563068-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-130563110-A-G		not specified	Uncertain significance (Oct 28, 2024)
3-130563112-C-T		not specified	Uncertain significance (Aug 17, 2021)
3-130563196-C-T		not specified	Uncertain significance (Jun 06, 2023)
3-130563203-C-T		not specified	Uncertain significance (Mar 23, 2022)
3-130563212-A-G		not specified	Uncertain significance (May 13, 2022)
3-130563268-C-A		not specified	Uncertain significance (Jan 07, 2025)
3-130563305-T-C		not specified	Uncertain significance (Oct 29, 2024)
3-130563326-G-A		not specified	Uncertain significance (Mar 08, 2024)
3-130563364-G-A		not specified	Uncertain significance (Nov 29, 2023)
3-130563367-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-130563383-A-C		not specified	Uncertain significance (Jun 16, 2024)
3-130563403-A-G		not specified	Uncertain significance (Sep 20, 2023)
3-130563446-A-G		not specified	Uncertain significance (May 11, 2022)
3-130563466-C-T		not specified	Uncertain significance (May 31, 2023)
3-130563467-G-A			Benign (Dec 26, 2018)
3-130563473-A-T		not specified	Uncertain significance (Feb 27, 2023)
3-130563474-C-T			Likely benign (Apr 01, 2022)
3-130563475-G-A		not specified	Uncertain significance (Mar 01, 2023)
3-130563478-G-A		not specified	Uncertain significance (Oct 06, 2021)
3-130563505-A-G		not specified	Uncertain significance (Jul 20, 2021)
3-130563534-G-T		not specified	Uncertain significance (Feb 19, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL6A6	protein_coding	protein_coding	ENST00000358511	36	117822

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.45e-46	0.0000885	123102	8	1533	124643	0.00620

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.419	1201	1.24e+3	0.967	0.0000674	14827
Missense in Polyphen		477	520.56	0.91633		6216
Synonymous	1.63	419	464	0.904	0.0000261	4429
Loss of Function	1.44	78	92.9	0.839	0.00000521	1180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0188	0.0183
Ashkenazi Jewish	0.00423	0.00418
East Asian	0.0173	0.0171
Finnish	0.00216	0.00209
European (Non-Finnish)	0.00417	0.00409
Middle Eastern	0.0173	0.0171
South Asian	0.0105	0.0104
Other	0.00573	0.00547

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Collagen VI acts as a cell-binding protein. {ECO:0000250}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Protein digestion and absorption - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);PI3K-Akt Signaling Pathway;Developmental Biology;Assembly of collagen fibrils and other multimeric structures;Signal Transduction;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Signaling by PDGF;Collagen formation;Extracellular matrix organization;NCAM signaling for neurite out-growth;NCAM1 interactions;Axon guidance;Signaling by Receptor Tyrosine Kinases (Consensus)

Intolerance Scores

• loftool: 0.155
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.42

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.155
• ghis: 0.453

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col6a6

Gene ontology

• Biological process: cell adhesion
• Cellular component: extracellular region;collagen trimer;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent conferring tensile strength