GPR12

G protein-coupled receptor 12, the group of Protein phosphatase 1 regulatory subunits|G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 13:26755200-26760786

Links

ENSG00000132975 ∙ NCBI:2835 ∙ OMIM:600752 ∙ HGNC:4466 ∙ Uniprot:P47775 ∙ 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 GPR12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR12 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
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	17	0	4

Variants in GPR12

This is a list of pathogenic ClinVar variants found in the GPR12 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-26758699-A-G			Benign (Nov 12, 2018)
13-26758836-G-C		not specified	Uncertain significance (Sep 03, 2024)
13-26758858-G-A		not specified	Uncertain significance (Aug 21, 2023)
13-26758933-C-G		not specified	Uncertain significance (Feb 26, 2024)
13-26759083-C-T		not specified	Uncertain significance (Dec 25, 2024)
13-26759102-G-T		not specified	Uncertain significance (Jun 28, 2022)
13-26759183-C-G		not specified	Uncertain significance (Jan 23, 2025)
13-26759275-C-G		not specified	Uncertain significance (Nov 24, 2024)
13-26759314-C-T		not specified	Uncertain significance (Nov 06, 2023)
13-26759330-C-T			Benign (Mar 29, 2018)
13-26759364-G-A		not specified	Uncertain significance (Feb 05, 2025)
13-26759449-A-G		not specified	Uncertain significance (May 31, 2023)
13-26759467-C-T		not specified	Uncertain significance (Nov 13, 2024)
13-26759487-A-G		not specified	Uncertain significance (Oct 10, 2023)
13-26759500-C-T		not specified	Uncertain significance (Dec 13, 2023)
13-26759515-A-G		not specified	Uncertain significance (Jan 17, 2024)
13-26759523-A-G		not specified	Uncertain significance (May 08, 2023)
13-26759533-T-A		not specified	Uncertain significance (Dec 14, 2023)
13-26759751-G-A		not specified	Uncertain significance (Apr 07, 2023)
13-26759770-C-T		not specified	Uncertain significance (Aug 26, 2024)
13-26759816-G-T		not specified	Uncertain significance (Oct 17, 2024)
13-26759823-T-G		not specified	Uncertain significance (Feb 28, 2023)
13-26759887-T-C			Benign (Jun 19, 2021)
13-26759947-T-C			Benign (Jun 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR12	protein_coding	protein_coding	ENST00000405846	1	5582

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.362	0.627	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	127	200	0.636	0.0000126	2139
Missense in Polyphen		50	82.746	0.60426		962
Synonymous	-0.188	100	97.6	1.02	0.00000754	748
Loss of Function	2.14	2	8.90	0.225	5.56e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes neurite outgrowth and blocks myelin inhibition in neurons (By similarity). Receptor with constitutive G(s) signaling activity that stimulates cyclic AMP production. {ECO:0000250}.
• Pathway: GPCRs, Class A Rhodopsin-like (Consensus)

Intolerance Scores

• loftool: 0.227
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.837
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr12
• Phenotype: liver/biliary system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

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