COL5A3

collagen type V alpha 3 chain, the group of Collagens

Basic information

Region (hg38): 19:9959561-10010504

Links

ENSG00000080573 ∙ NCBI:50509 ∙ OMIM:120216 ∙ HGNC:14864 ∙ Uniprot:P25940 ∙ 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 COL5A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL5A3 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	2	6
missense			111	8	2	121
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	111	12	4

Variants in COL5A3

This is a list of pathogenic ClinVar variants found in the COL5A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9960508-G-A		not specified	Likely benign (Jun 21, 2022)
19-9960511-C-T		not specified	Uncertain significance (May 12, 2024)
19-9960539-T-G		not specified	Uncertain significance (Nov 09, 2021)
19-9960541-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-9960653-G-C		not specified	Uncertain significance (Mar 25, 2024)
19-9960679-G-T		not specified	Uncertain significance (May 10, 2024)
19-9960686-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-9960691-G-T		not specified	Uncertain significance (Jun 23, 2021)
19-9960733-C-T		not specified	Uncertain significance (Feb 21, 2024)
19-9960840-G-C		not specified	Uncertain significance (Apr 13, 2023)
19-9960872-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-9960875-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-9962887-C-G		not specified	Uncertain significance (Feb 10, 2022)
19-9966340-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-9966354-C-G		not specified	Uncertain significance (Mar 18, 2024)
19-9966377-C-T			Likely benign (Nov 01, 2022)
19-9966378-C-T		not specified	Uncertain significance (Jan 26, 2023)
19-9966548-G-A		not specified	Uncertain significance (May 23, 2023)
19-9966572-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-9966691-G-C		not specified	Uncertain significance (Jun 16, 2023)
19-9967385-G-C		not specified	Uncertain significance (Sep 01, 2021)
19-9967905-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-9968034-C-A		not specified	Uncertain significance (May 30, 2024)
19-9968054-A-G		not specified	Uncertain significance (Mar 21, 2024)
19-9968062-A-C		not specified	Uncertain significance (Jul 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL5A3	protein_coding	protein_coding	ENST00000264828	67	50911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.35e-20	1.00	125585	0	163	125748	0.000648

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.492	946	990	0.956	0.0000583	10773
Missense in Polyphen		63	81.671	0.77138		799
Synonymous	0.317	386	394	0.980	0.0000240	3841
Loss of Function	4.99	51	107	0.479	0.00000533	1258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000879	0.000877
Ashkenazi Jewish	0.00	0.00
East Asian	0.000740	0.000707
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000657	0.000633
Middle Eastern	0.000740	0.000707
South Asian	0.00166	0.00147
Other	0.00102	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin.
• Pathway: Protein digestion and absorption - Homo sapiens (human);miRNA targets in ECM and membrane receptors;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Intolerance Scores

• loftool: 0.0606
• rvis_EVS: 0.14
• rvis_percentile_EVS: 63.58

Haploinsufficiency Scores

• pHI: 0.454
• hipred: Y
• hipred_score: 0.577
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col5a3
• Phenotype: endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell adhesion;cell-matrix adhesion;extracellular matrix organization;collagen fibril organization;skin development
• Cellular component: extracellular region;collagen type V trimer;extracellular space;endoplasmic reticulum lumen;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;collagen binding;heparin binding;extracellular matrix structural constituent conferring tensile strength;proteoglycan binding