COL15A1

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

Basic information

Region (hg38): 9:98943179-99070787

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.

not_specified (197 variants)
COL15A1-related_disorder (45 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. These statistics are base on transcript: NM_000001855.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				16 clinvar	5 clinvar	21
missense			185 clinvar	17 clinvar	17 clinvar	219
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	185	33	22

Loading clinvar variants...

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