COL15A1

collagen type XV alpha 1 chain, the group of Collagen proteoglycans|Collagens

Basic information

Region (hg38): 9:98943178-99070792

Links

ENSG00000204291 ∙ NCBI:1306 ∙ OMIM:120325 ∙ HGNC:2192 ∙ Uniprot:P39059 ∙ 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 COL15A1 gene.

• Inborn genetic diseases (57 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COL15A1 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				2	2	4
missense			53	5	4	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	7	6

Variants in COL15A1

This is a list of pathogenic ClinVar variants found in the COL15A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-98944156-T-G			not provided (-)
9-98944225-T-C		COL15A1-related disorder	Likely benign (Feb 22, 2019)
9-98944241-G-T		not specified	Uncertain significance (Dec 11, 2023)
9-98944248-C-T		not specified	Uncertain significance (May 31, 2023)
9-98944259-C-A		COL15A1-related disorder	Likely benign (Jun 13, 2019)
9-98985597-C-A		not specified	Uncertain significance (Dec 06, 2021)
9-98985603-A-G		COL15A1-related disorder	Benign (Mar 12, 2019)
9-98985606-G-A		not specified	Uncertain significance (Jun 08, 2022)
9-98985635-T-C		COL15A1-related disorder	Likely benign (Jul 11, 2019)
9-98985671-C-T		COL15A1-related disorder	Likely benign (Jun 12, 2019)
9-98985672-G-C		not specified	Uncertain significance (Aug 28, 2023)
9-98985681-G-A		not specified	Uncertain significance (Aug 30, 2022)
9-98985723-T-C		not specified	Uncertain significance (Mar 11, 2022)
9-98985737-C-T		COL15A1-related disorder	Likely benign (Jun 18, 2019)
9-98985739-C-T		not specified	Uncertain significance (Sep 01, 2021)
9-98985745-G-A		not specified	Uncertain significance (Jun 28, 2022)
9-98985750-G-A		COL15A1-related disorder	Likely benign (Apr 18, 2022)
9-98985766-G-C		not specified	Uncertain significance (Feb 21, 2024)
9-98985862-G-A		not specified	Uncertain significance (Jun 23, 2023)
9-98985925-T-G		not specified	Uncertain significance (Jan 03, 2024)
9-98985930-G-T		not specified	Uncertain significance (Jul 13, 2021)
9-98985952-G-A		COL15A1-related disorder	Benign (Oct 21, 2019)
9-98986000-G-A		not specified	Uncertain significance (Mar 31, 2022)
9-98986035-T-C		COL15A1-related disorder	Benign (Jun 07, 2019)
9-98986074-A-G		COL15A1-related disorder	Benign (Oct 17, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COL15A1	protein_coding	protein_coding	ENST00000375001	42	127609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.54e-8	1.00	125183	1	564	125748	0.00225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.120	798	808	0.988	0.0000437	8846
Missense in Polyphen		296	311.87	0.94912		3253
Synonymous	-0.898	341	321	1.06	0.0000202	2952
Loss of Function	5.05	27	73.8	0.366	0.00000372	866

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00267	0.00265
Ashkenazi Jewish	0.00794	0.00797
East Asian	0.000879	0.000870
Finnish	0.00185	0.00185
European (Non-Finnish)	0.00179	0.00178
Middle Eastern	0.000879	0.000870
South Asian	0.00464	0.00462
Other	0.00277	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Structural protein that stabilizes microvessels and muscle cells, both in heart and in skeletal muscle. {ECO:0000269|PubMed:10049780}.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Assembly of collagen fibrils and other multimeric structures;Collagen chain trimerization;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;Integrin (Consensus)

Intolerance Scores

• loftool: 0.0931
• rvis_EVS: 1.84
• rvis_percentile_EVS: 97.1

Haploinsufficiency Scores

• pHI: 0.211
• hipred: N
• hipred_score: 0.280
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0880

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Col15a1
• Phenotype: muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: col15a1a
• Affected structure: primary motor neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: angiogenesis;cell adhesion;signal transduction;cell differentiation;extracellular matrix organization;collagen catabolic process
• Cellular component: extracellular region;collagen type XV trimer;extracellular space;endoplasmic reticulum lumen;integral component of membrane;extracellular matrix;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent;extracellular matrix structural constituent conferring tensile strength