GPR15

protein-coding

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

Gene summary

This gene encodes a G protein-coupled receptor that acts as a chemokine receptor for human immunodeficiency virus type 1 and 2. The encoded protein localizes to the cell membrane. [provided by RefSeq, Nov 2012]

MANE transcript

NM_005290.4

Inheritance

—

ClinVar variants

U:51B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr3:98,531,978-98,534,681

External References & Databases

Ensembl (ENSG00000154165)

Transcript & Mutation Effects

hg38 • Region Span ~2.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GPR15 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005290.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			51 clinvar	3 clinvar	1 clinvar	55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	4	2	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005290.4	RefSeq	NP_005281.1	1	MANE Select
ENST00000284311.5	Ensembl	ENSP00000284311.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

GPCRs, Class A Rhodopsin-like
Signaling by GPCR
Signal Transduction
G alpha (s) signalling events
GPCR downstream signalling

Biological Process

G protein-coupled receptor signaling pathway
viral entry into host cell
T cell migration

Molecular Function

virus receptor activity
G protein-coupled receptor activity
protein binding
coreceptor activity

Cellular Component

endosome
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000284311
Coding exons: 1
Length: 1218
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0444	197	195	1.01	0.00000998	2349
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable chemokine receptor. Alternative coreceptor with CD4 for HIV-1 infection.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.573
RVIS EVS: 0.49
RVIS percentile EVS: 79.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.752

Gene Damage Prediction

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