GPR89A

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

Basic information

Region (hg38): 1:145607988-145670650

Links

ENSG00000117262 ∙ NCBI:653519 ∙ OMIM:612821 ∙ HGNC:31984 ∙ Uniprot:B7ZAQ6 ∙ 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 GPR89A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR89A 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in GPR89A

This is a list of pathogenic ClinVar variants found in the GPR89A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145623058-C-T		not specified	Uncertain significance (Jun 10, 2024)
1-145623059-G-A		not specified	Uncertain significance (Feb 06, 2025)
1-145623078-G-T		not specified	Uncertain significance (May 30, 2024)
1-145623142-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-145623622-A-G		not specified	Uncertain significance (Dec 27, 2023)
1-145646196-T-C		not specified	Uncertain significance (Nov 25, 2024)
1-145647181-A-G		not specified	Uncertain significance (Jul 31, 2023)
1-145663354-G-A		not specified	Uncertain significance (Dec 17, 2024)
1-145663357-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-145663368-G-T		not specified	Uncertain significance (Mar 25, 2024)
1-145663375-T-G		not specified	Uncertain significance (Dec 18, 2023)
1-145663399-T-C		not specified	Uncertain significance (Oct 01, 2024)
1-145665613-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-145665650-A-G		not specified	Uncertain significance (Aug 28, 2023)
1-145669855-G-A		not specified	Uncertain significance (Oct 26, 2021)
1-145669868-G-A		not specified	Uncertain significance (Jan 19, 2025)
1-145669876-A-G		not specified	Uncertain significance (Nov 13, 2024)
1-145669886-A-C		not specified	Uncertain significance (Dec 31, 2024)
1-145669937-A-G		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR89A	protein_coding	protein_coding	ENST00000313835	14	62693

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.66e-14	0.0167	125643	1	90	125734	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.344	130	142	0.919	0.00000723	3002
Missense in Polyphen		27	30.854	0.87508		735
Synonymous	-0.868	57	49.2	1.16	0.00000241	847
Loss of Function	-0.0929	20	19.6	1.02	0.00000122	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000525	0.000518
Ashkenazi Jewish	0.00	0.00
East Asian	0.00127	0.00125
Finnish	0.000186	0.000139
European (Non-Finnish)	0.000281	0.000255
Middle Eastern	0.00127	0.00125
South Asian	0.000774	0.000719
Other	0.000400	0.000326

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:12761501, ECO:0000269|PubMed:18794847}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.380
• ghis: 0.529

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;positive regulation of I-kappaB kinase/NF-kappaB signaling;intracellular pH reduction
• Cellular component: integral component of membrane;Golgi-associated vesicle membrane;Golgi cisterna membrane
• Molecular function: voltage-gated anion channel activity