GPR39

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

Basic information

Region (hg38): 2:132416805-132646582

Links

ENSG00000183840 ∙ NCBI:2863 ∙ OMIM:602886 ∙ HGNC:4496 ∙ Uniprot:O43194 ∙ 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 GPR39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR39 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
missense			25	3	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	27	3	4

Variants in GPR39

This is a list of pathogenic ClinVar variants found in the GPR39 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-132417070-G-C		not specified	Uncertain significance (Aug 26, 2022)
2-132417230-A-G		not specified	Uncertain significance (Sep 14, 2023)
2-132417275-C-T		not specified	Uncertain significance (Feb 17, 2022)
2-132417417-C-A		not specified	Uncertain significance (Mar 25, 2024)
2-132417445-A-G		not specified	Likely benign (Dec 28, 2022)
2-132417478-G-A		not specified	Uncertain significance (Jul 26, 2022)
2-132417483-G-A			Benign (Jun 10, 2018)
2-132417634-C-A		not specified	Uncertain significance (Oct 25, 2023)
2-132417641-A-G		not specified	Uncertain significance (May 02, 2024)
2-132417663-G-T		not specified	Uncertain significance (Apr 19, 2024)
2-132417664-T-G		not specified	Uncertain significance (Apr 19, 2024)
2-132417677-A-G			Benign (Aug 20, 2018)
2-132417763-A-G		not specified	Uncertain significance (Jan 23, 2024)
2-132417811-C-G		not specified	Uncertain significance (Dec 05, 2022)
2-132417853-A-C		not specified	Uncertain significance (Feb 10, 2022)
2-132645123-C-A			Benign (Jul 10, 2017)
2-132645124-G-T		not specified	Uncertain significance (Dec 21, 2023)
2-132645145-A-C		not specified	Uncertain significance (Jun 07, 2024)
2-132645199-T-C		not specified	Uncertain significance (Mar 02, 2023)
2-132645284-C-T		not specified	Uncertain significance (Aug 22, 2023)
2-132645310-G-C		not specified	Uncertain significance (Apr 19, 2024)
2-132645337-C-A		not specified	Uncertain significance (Dec 02, 2022)
2-132645338-T-G		not specified	Uncertain significance (Dec 02, 2022)
2-132645341-A-C		not specified	Likely benign (Aug 21, 2023)
2-132645341-A-G		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR39	protein_coding	protein_coding	ENST00000329321	2	229986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.81e-9	0.0462	125671	1	76	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.359	285	303	0.942	0.0000210	2954
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000569	0.000569
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.00144	0.00141
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.832
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.0978
• hipred: N
• hipred_score: 0.301
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.202

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr39
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;metal ion binding