COL6A5

protein-coding

collagen type VI alpha 5 chain, the group of Collagens

Gene summary

This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

Previous symbols:

COL29A1

MANE transcript

NM_001278298.2

Inheritance

—

ClinVar variants

U:321B:66

Top phenotype

COL6A5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr3:130,345,516-130,484,846

External References & Databases

Ensembl (ENSG00000172752)

Transcript & Mutation Effects

hg38 • Region Span ~139.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COL6A5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 355

not providedTotal: 34

COL6A5-related disorderTotal: 12

COL6A5 POLYMORPHISMTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001278298.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				7 clinvar	2 clinvar	9
missense			317 clinvar	48 clinvar	4 clinvar	369
nonsense			1 clinvar	2 clinvar	1 clinvar	4
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar	1 clinvar	1 clinvar	4
Total	0	0	321	58	8	387

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001278298.2	RefSeq	NP_001265227.1	40	MANE Select
ENST00000373157.9	Ensembl	ENSP00000362250.5	40	MANE Select
NM_153264.7	RefSeq	NP_694996.5	39	Standard
ENST00000312481.11	Ensembl	ENSP00000309762.7	40	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

cell adhesion

Molecular Function

protein binding
extracellular matrix structural constituent conferring tensile strength

Cellular Component

extracellular region
collagen trimer
collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265379
Coding exons: 40
Length: 139330
Individuals with no LoFs: 117430
Homozygous LoFs: 263
Heterozygous LoFs: 6923
Defined: 124616
p: 0.0293

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.18	1093	1.32e+3	0.831	0.0000665	17226
Missense (PolyPhen)		280	361.38	0.7748		4791
Synonymous	2.94	393	475	0.828	0.0000248	4952
Loss of Function	2.25	83	108	0.766	0.00000578	1432

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0075	0.0073	notable
Latino/Admixed American	0.12	0.12	notable
Ashkenazi Jewish	0.014	0.013	notable
East Asian	0.00096	0.00095	rare
Finnish	0.027	0.027	notable
European (Non-Finnish)	0.017	0.016	notable
South Asian	0.020	0.020	notable
Other	0.028	0.027	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Collagen VI acts as a cell-binding protein. {ECO:0000250}.;
Disease: DISEASE: Note=Patients affected by atopic dermatitis display an abnormal distribution of COL29A1 mRNA and protein in skin suggesting that COL29A1 may be involved in the pathogenesis of the disease.;

Recessive Scores

pRec: 0.0631

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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