GPR15

G protein-coupled receptor 15, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 3:98531977-98534681

Links

ENSG00000154165 ∙ NCBI:2838 ∙ OMIM:601166 ∙ HGNC:4469 ∙ Uniprot:P49685 ∙ 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 GPR15 gene.

• Inborn genetic diseases (12 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR15 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				1	1	2
missense			13		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	2

Variants in GPR15

This is a list of pathogenic ClinVar variants found in the GPR15 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-98532064-G-C		not specified	Uncertain significance (Dec 06, 2023)
3-98532080-C-T		not specified	Uncertain significance (Feb 10, 2022)
3-98532083-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-98532094-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-98532106-A-T		not specified	Uncertain significance (Nov 21, 2023)
3-98532227-G-A			Uncertain significance (Oct 06, 2017)
3-98532233-T-G		not specified	Uncertain significance (Sep 01, 2021)
3-98532255-T-A		not specified	Uncertain significance (Dec 07, 2021)
3-98532333-G-T		not specified	Uncertain significance (Dec 01, 2022)
3-98532367-A-G			Benign (Feb 25, 2018)
3-98532368-T-A		not specified	Uncertain significance (Jun 05, 2023)
3-98532380-A-C		not specified	Uncertain significance (Feb 10, 2022)
3-98532399-C-T			Likely benign (Sep 01, 2022)
3-98532470-G-A		not specified	Uncertain significance (Jul 30, 2023)
3-98532476-A-G		not specified	Uncertain significance (Jul 19, 2023)
3-98532488-T-C		not specified	Uncertain significance (Jan 23, 2023)
3-98532771-C-T			Benign (Feb 25, 2018)
3-98532772-G-C		not specified	Uncertain significance (Dec 21, 2023)
3-98532788-T-A		not specified	Uncertain significance (May 01, 2022)
3-98532841-C-T		not specified	Uncertain significance (Jan 22, 2024)
3-98532842-G-A		not specified	Likely benign (Sep 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR15	protein_coding	protein_coding	ENST00000284311	1	1218

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000111	0.204	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0444	197	195	1.01	0.00000998	2349
Missense in Polyphen		74	72.352	1.0228		885
Synonymous	-0.113	81	79.7	1.02	0.00000406	740
Loss of Function	-0.0525	9	8.83	1.02	4.54e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable chemokine receptor. Alternative coreceptor with CD4 for HIV-1 infection.
• Pathway: GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.573
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.38

Haploinsufficiency Scores

• pHI: 0.0921
• hipred: N
• hipred_score: 0.219
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.752

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr15
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; immune system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;viral entry into host cell;T cell migration
• Cellular component: endosome;plasma membrane;integral component of plasma membrane
• Molecular function: virus receptor activity;G protein-coupled receptor activity;protein binding;coreceptor activity