GPR39

protein-coding

G protein-coupled receptor 39, the group of G protein-coupled receptors, Class A orphans

Gene summary

This gene is a member of the ghrelin receptor family and encodes a rhodopsin-type G-protein-coupled receptor (GPCR). The encoded protein is involved in zinc-dependent signaling in epithelial tissue in intestines, prostate and salivary glands. The protein may also be involved in the pathophysiology of depression. [provided by RefSeq, Jun 2016]

MANE transcript

NM_001508.3

Inheritance

—

ClinVar variants

U:76B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.2

Max pathogenic AF

—

Genomic locus

chr2:132,416,805-132,646,582

External References & Databases

Ensembl (ENSG00000183840)

Transcript & Mutation Effects

hg38 • Region Span ~229.8 kb

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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 GPR39 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001508.3. 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		2 clinvar	3
missense			74 clinvar	6 clinvar	1 clinvar	81
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	6	3	85

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_001508.3	RefSeq	NP_001499.1	2	MANE Select
ENST00000329321.4	Ensembl	ENSP00000327417.3	2	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
Class A/1 (Rhodopsin-like receptors)

Biological Process

G protein-coupled receptor signaling pathway

Molecular Function

G protein-coupled receptor activity
metal ion binding

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329321
Coding exons: 2
Length: 229986
Individuals with no LoFs: 125671
Homozygous LoFs: 1
Heterozygous LoFs: 76
Defined: 125748
p: 0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.359	285	303	0.942	0.0000210	2954
Missense (PolyPhen)		88	111.8	0.78713		1202
Synonymous	-0.131	143	141	1.01	0.0000110	942
Loss of Function	-0.575	12	10.0	1.20	4.33e-7	113

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.0014	0.0014	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Zn(2+) acts as an agonist. This receptor mediates its action by association with G proteins that activate a phosphatidylinositol-calcium second messenger system. Its effect is mediated mainly through G(q)-alpha and G(12)/G(13) proteins. Involved in regulation of body weight, gastrointestinal mobility, hormone secretion and cell death (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.832
RVIS EVS: -0.09
RVIS percentile EVS: 47.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.202

Gene Damage Prediction

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