GPR89B

G protein-coupled receptor 89B, the group of 7TM uncharacterized proteins

Basic information

Region (hg38): 1:147928393-147993592

Previous symbols: [ "GPR89", "GPR89C" ]

Links

ENSG00000188092 ∙ NCBI:51463 ∙ OMIM:612806 ∙ HGNC:13840 ∙ Uniprot:P0CG08 ∙ 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 GPR89B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR89B 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in GPR89B

This is a list of pathogenic ClinVar variants found in the GPR89B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-147928551-C-G		not specified	Uncertain significance (Nov 09, 2024)
1-147936663-C-T		not specified	Uncertain significance (Oct 09, 2024)
1-147938715-T-C		not specified	Uncertain significance (Jan 24, 2024)
1-147938718-G-A		not specified	Uncertain significance (May 27, 2022)
1-147938732-C-G		not specified	Uncertain significance (Jul 14, 2021)
1-147938751-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-147943477-T-G		not specified	Uncertain significance (Jan 18, 2023)
1-147943497-T-C		not specified	Uncertain significance (Dec 23, 2024)
1-147943532-A-G		not specified	Uncertain significance (May 31, 2023)
1-147944009-G-A		not specified	Uncertain significance (Jun 10, 2022)
1-147944020-T-C		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR89B	protein_coding	protein_coding	ENST00000314163	14	65248

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000215	0.754	125417	5	324	125746	0.00131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.808	53	72.3	0.733	0.00000390	3022
Missense in Polyphen		3	10.325	0.29057		743
Synonymous	0.432	22	24.7	0.889	0.00000123	854
Loss of Function	1.02	7	10.6	0.661	7.22e-7	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00974	0.00831
Ashkenazi Jewish	0.00271	0.00199
East Asian	0.000469	0.000435
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000692	0.000659
Middle Eastern	0.000469	0.000435
South Asian	0.00306	0.00242
Other	0.00143	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Voltage dependent anion channel required for acidification and functions of the Golgi apparatus that may function in counter-ion conductance. {ECO:0000250, ECO:0000269|PubMed:18794847}.

Haploinsufficiency Scores

• pHI: 0.211
• hipred: N
• hipred_score: 0.380
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: 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: Gpr89
• Phenotype: pigmentation phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; immune system phenotype; hearing/vestibular/ear phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Gene ontology

• Biological process: protein transport;inorganic anion transport;ion transmembrane transport;regulation of ion transmembrane transport;intracellular pH reduction
• Cellular component: integral component of membrane;Golgi cisterna membrane
• Molecular function: voltage-gated anion channel activity