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.

• not_specified (326 variants)
• not_provided (49 variants)
• COL6A6-related_disorder (3 variants)

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. These statistics are base on transcript: NM_001102608.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				9	9	18
missense			307	30	7	344
nonsense			1	1		2
start loss						0
frameshift			2	1		3
splice donor/acceptor (+/-2bp)		1		1		2
Total	0	1	310	42	16

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