COL6A5

collagen type VI alpha 5 chain, the group of Collagens

Basic information

Region (hg38): 3:130345516-130484846

Previous symbols: [ "COL29A1" ]

Links

ENSG00000172752 ∙ NCBI:256076 ∙ OMIM:611916 ∙ HGNC:26674 ∙ Uniprot:A8TX70 ∙ 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 COL6A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL6A5 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				4	3	7
missense			174	28	5	207
nonsense					1	1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1		1	2
splice region			1	1	1	3
non coding						0
Total	0	0	176	32	10

Variants in COL6A5

This is a list of pathogenic ClinVar variants found in the COL6A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-130373645-A-G		not specified	Uncertain significance (Nov 24, 2024)
3-130376243-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-130376262-C-T			Likely benign (Nov 01, 2024)
3-130376284-G-A		not specified	Uncertain significance (Jan 03, 2022)
3-130376321-C-T		not specified	Uncertain significance (Oct 26, 2021)
3-130376326-A-G		not specified	Uncertain significance (Oct 07, 2024)
3-130376350-C-A		not specified	Uncertain significance (Dec 03, 2024)
3-130376371-C-T		not specified	Uncertain significance (Nov 22, 2023)
3-130376398-G-A		not specified	Likely benign (Feb 07, 2023)
3-130376417-A-G		not specified	Uncertain significance (Jul 31, 2024)
3-130376426-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-130376435-G-T		not specified	Uncertain significance (Nov 28, 2024)
3-130376463-G-C		not specified	Uncertain significance (Nov 08, 2024)
3-130376485-G-T		not specified	Uncertain significance (Jul 26, 2022)
3-130376506-G-A		not specified	Uncertain significance (Jul 27, 2024)
3-130376578-A-G		not specified	Uncertain significance (Jun 21, 2023)
3-130376649-C-T			Benign (Apr 03, 2018)
3-130376651-G-A		not specified	Uncertain significance (Oct 22, 2021)
3-130376666-C-T		not specified	Uncertain significance (Nov 10, 2024)
3-130376668-G-A		not specified	Uncertain significance (Apr 08, 2022)
3-130376672-G-C		not specified	Uncertain significance (Jul 14, 2024)
3-130376738-G-A		not specified	Uncertain significance (Sep 12, 2023)
3-130376827-G-C		not specified	Uncertain significance (Feb 28, 2024)
3-130379501-T-G		not specified	Uncertain significance (Jan 16, 2024)
3-130379531-A-C		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL6A5	protein_coding	protein_coding	ENST00000265379	40	139330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.61e-45	0.00715	117430	263	6923	124616	0.0293

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.18	1093	1.32e+3	0.831	0.0000665	17226
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.124	0.124
Ashkenazi Jewish	0.0136	0.0129
East Asian	0.000955	0.000946
Finnish	0.0272	0.0271
European (Non-Finnish)	0.0167	0.0163
Middle Eastern	0.000955	0.000946
South Asian	0.0204	0.0198
Other	0.0280	0.0270

dbNSFP

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.
• 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)

Recessive Scores

• pRec: 0.0631

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col6a5

Gene ontology

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