GPR139

G protein-coupled receptor 139, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 16:20028238-20073890

Links

ENSG00000180269 ∙ NCBI:124274 ∙ OMIM:618448 ∙ HGNC:19995 ∙ Uniprot:Q6DWJ6 ∙ 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 GPR139 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR139 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						0
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in GPR139

This is a list of pathogenic ClinVar variants found in the GPR139 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20031749-T-C		not specified	Uncertain significance (May 16, 2024)
16-20031808-G-A		not specified	Uncertain significance (Feb 26, 2024)
16-20031999-C-T		not specified	Uncertain significance (Jan 31, 2024)
16-20032025-G-T		not specified	Uncertain significance (Dec 18, 2023)
16-20032106-A-G		not specified	Uncertain significance (Aug 02, 2021)
16-20032121-T-A		not specified	Uncertain significance (Nov 02, 2023)
16-20032123-T-C		not specified	Uncertain significance (Dec 17, 2023)
16-20032184-T-C		not specified	Uncertain significance (Dec 13, 2022)
16-20032217-C-T		not specified	Uncertain significance (May 24, 2024)
16-20032277-A-T		not specified	Uncertain significance (Mar 12, 2024)
16-20032330-C-A		not specified	Uncertain significance (Dec 02, 2022)
16-20032351-A-G		not specified	Uncertain significance (Dec 15, 2022)
16-20032373-G-T		not specified	Uncertain significance (Jun 09, 2022)
16-20032384-G-A		not specified	Uncertain significance (Jul 09, 2021)
16-20032435-G-A		not specified	Uncertain significance (May 08, 2023)
16-20032496-C-T		not specified	Likely benign (May 09, 2024)
16-20032555-A-C		not specified	Uncertain significance (Dec 13, 2022)
16-20032562-A-G		not specified	Uncertain significance (Nov 10, 2022)
16-20073516-C-A		not specified	Uncertain significance (Jan 23, 2023)
16-20073532-G-A		not specified	Uncertain significance (Oct 06, 2021)
16-20073576-A-C		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR139	protein_coding	protein_coding	ENST00000570682	2	42433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0369	0.932	125731	0	10	125741	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.911	166	202	0.820	0.0000119	2320
Missense in Polyphen		80	107.48	0.74433		1208
Synonymous	-0.429	91	85.9	1.06	0.00000542	700
Loss of Function	1.87	4	10.6	0.379	4.54e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor. Seems to act through a G(q/11)-mediated pathway.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.401
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.278
• hipred: Y
• hipred_score: 0.507
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.203

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr139

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;neuropeptide signaling pathway
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: neuropeptide receptor activity;protein dimerization activity