GPR78

G protein-coupled receptor 78, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 4:8558725-8619761

Links

ENSG00000155269 ∙ NCBI:27201 ∙ OMIM:606921 ∙ HGNC:4528 ∙ Uniprot:Q96P69 ∙ 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 GPR78 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR78 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	3	4
missense			40	2		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	3	3

Variants in GPR78

This is a list of pathogenic ClinVar variants found in the GPR78 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-8580988-C-T			Benign (Mar 29, 2018)
4-8580989-C-T		not specified	Uncertain significance (Sep 29, 2022)
4-8580992-G-T		not specified	Uncertain significance (Jun 23, 2021)
4-8581017-T-C		not specified	Uncertain significance (May 11, 2022)
4-8581034-G-A		not specified	Uncertain significance (Sep 16, 2021)
4-8581097-C-G		not specified	Uncertain significance (Oct 26, 2022)
4-8581098-G-A		not specified	Uncertain significance (Dec 14, 2022)
4-8581130-C-T			Likely benign (Sep 03, 2018)
4-8581134-G-A		not specified	Uncertain significance (Aug 22, 2022)
4-8581136-C-T		not specified	Uncertain significance (Jan 04, 2024)
4-8581145-C-A		not specified	Uncertain significance (Jun 11, 2024)
4-8581159-C-G		not specified	Uncertain significance (Mar 06, 2023)
4-8581163-C-T		not specified	Uncertain significance (Sep 29, 2023)
4-8581168-C-G		not specified	Uncertain significance (Jun 20, 2024)
4-8581186-G-A		not specified	Uncertain significance (Aug 22, 2023)
4-8581208-C-T		not specified	Uncertain significance (Feb 15, 2023)
4-8581259-G-T		not specified	Uncertain significance (Sep 01, 2021)
4-8581275-C-T		not specified	Uncertain significance (Aug 04, 2023)
4-8581286-G-A		not specified	Uncertain significance (Aug 26, 2022)
4-8581306-G-A			Benign (Mar 29, 2018)
4-8581340-C-T		not specified	Uncertain significance (Jan 18, 2022)
4-8581401-C-G		not specified	Uncertain significance (Sep 29, 2022)
4-8581409-G-T		not specified	Uncertain significance (Apr 18, 2023)
4-8581441-C-G		not specified	Uncertain significance (Mar 28, 2024)
4-8581452-C-T		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR78	protein_coding	protein_coding	ENST00000382487	3	61035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000268	0.180	125534	0	4	125538	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.25	301	246	1.22	0.0000178	2219
Missense in Polyphen		81	70.283	1.1525		721
Synonymous	-1.90	146	120	1.22	0.00000889	843
Loss of Function	-0.308	8	7.11	1.12	3.44e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000880
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor. Displays a significant level of constitutive activity. Its effect is mediated by G(s)-alpha protein that stimulate adenylate cyclase, resulting in an elevation of intracellular cAMP. {ECO:0000269|PubMed:17363172}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.654
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.76

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.170
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.245

Gene Damage Prediction

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

Gene ontology

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