GPR156

G protein-coupled receptor 156, the group of G protein-coupled receptors, Class C orphans

Basic information

Region (hg38): 3:120164645-120285222

Links

ENSG00000175697 ∙ NCBI:165829 ∙ OMIM:610464 ∙ HGNC:20844 ∙ Uniprot:Q8NFN8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal recessive 121 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 121	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	36928819; 37814107

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPR156 gene.

• not_specified (107 variants)
• GPR156-related_disorder (3 variants)
• Hearing_loss,_autosomal_recessive_121 (3 variants)
• Hearing_loss,_autosomal_recessive (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR156 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153002.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1		2		3
missense			97	11		108
nonsense						0
start loss						0
frameshift		2				2
splice donor/acceptor (+/-2bp)						0
Total	0	3	97	13	0

Highest pathogenic variant AF is 0.00000273715

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR156	protein_coding	protein_coding	ENST00000464295	9	120450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.25e-12	0.507	125615	0	133	125748	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	382	444	0.861	0.0000232	5283
Missense in Polyphen		114	138.96	0.8204		1800
Synonymous	0.628	167	178	0.940	0.00000920	1686
Loss of Function	1.40	23	31.5	0.730	0.00000153	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000919	0.000913
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000664	0.000659
Middle Eastern	0.000218	0.000217
South Asian	0.00105	0.00105
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0767

Intolerance Scores

• loftool: 0.393
• rvis_EVS: 1.4
• rvis_percentile_EVS: 94.76

Haploinsufficiency Scores

• pHI: 0.0567
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr156

Gene ontology

• Biological process: gamma-aminobutyric acid signaling pathway
• Cellular component: plasma membrane;G protein-coupled receptor heterodimeric complex
• Molecular function: G protein-coupled GABA receptor activity