GPR98 G protein-coupled receptor 98 [Homo sapiens (human)] - Gene

Summary

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Official Symbol: GPR98provided by HGNC
Official Full Name: G protein-coupled receptor 98provided by HGNC
Primary source: HGNC:17416
See related: Ensembl:ENSG00000164199; HPRD:09111; MIM:602851; Vega:OTTHUMG00000162668
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FEB4; MASS1; USH2B; USH2C; VLGR1; VLGR1b
Summary: This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]

Genomic context

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Location :: 5q13

Sequence :: Chromosome: 5; NC_000005.9 (89854617..90460033)

See GPR98 in Epigenomics, MapViewer

Chromosome 5 - NC_000005.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

genetic association studies in postmenopausal Japanese women: Study found association between an SNP in GPR98 (rs10514346) and bone mineral density in this population; data suggest that Gpr98 signaling pathway regulates bone metabolism.
Title: GPR98/Gpr98 gene is involved in the regulation of human and mouse bone mineral density.
Mutation found in USH2A, GPR98, or DFNB31 account for the vast majority of USH2 patients and their analysis provide a robust pathway for routine molecular diagnosis.
Title: Non-USH2A mutations in USH2 patients.
Observational study of genetic testing. (HuGE Navigator)
Title: Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Clinical trial and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
Observational study of gene-disease association. (HuGE Navigator)
Title: Replication of previous genome-wide association studies of bone mineral density in premenopausal American women.
Observational study of gene-disease association and genetic testing. (HuGE Navigator)
Title: Microarray-based mutation analysis of 183 Spanish families with Usher syndrome.
study describes for the first time two male patients with Usher syndrome type 2 with novel GPR98 mutations
Title: GPR98 mutations cause Usher syndrome type 2 in males.
GPR98 genes and the phenotypic heterogeneity and particularly the severe ocular affection first observed in one Usher syndrome patient.
Title: Identification of two new mutations in the GPR98 and the PDE6B genes segregating in a Tunisian family.

Submit: New GeneRIF Correction See all (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Usher syndrome type II is characterized by congenital (i.e., prelingual) bilateral sensorineural hearing loss that is mild to moderate in the low frequencies and severe to profound in the higher frequencies, intact vestibular responses, and retinitis pigmentosa (RP). RP is progressive, bilateral, symmetric retinal degeneration that begins with night blindness and constricted visual fields (tunnel vision) and eventually includes decreased central visual acuity; the rate and degree of vision loss vary within and among families.

Diagnosis Testing

The diagnosis of Usher syndrome type II is established on clinical grounds using electrophysiologic and subjective tests of hearing and retinal function. Three genes are known to be associated with Usher syndrome type II: USH2A (accounting for 80% of cases), GPR98 (VLGR1) (~15% of cases), and DFNB31 (<5% of cases). A fourth locus has been provisionally mapped to 15q.

Genetic Counseling

Usher syndrome type II is inherited in an autosomal recessive manner. Each subsequent pregnancy of a couple who has had a child with Usher syndrome type II has a 25% chance of resulting in an affected child, a 50% chance of resulting in an unaffected child who is a carrier, and a 25% chance of resulting in an unaffected child who is not a carrier. Prenatal testing is possible for pregnancies at increased risk if the disease-causing mutations have been identified in the family.

References

PMID: 20301515

NHGRI GWAS Catalog

Genome-wide association with bone mass and geometry in the Framingham Heart Study.

Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.

Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.

Pathways from BioSystems

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GPCRs, Other, organism-specific biosystem (from WikiPathways)
GPCRs, Other, organism-specific biosystemThis pathway was created using the GPCRDB (Horn et al., 1998), http://www.cmbi.kun.nl/7tm/. The groupings are based on the GPCR phylogenetic tree available from the GPCRDB and the training sets used ...

General gene information

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Markers

D3S3647 (e-PCR), detects polymorphism
- UniSTS:53253

SHGC-105215 (e-PCR)
- UniSTS:169238

RH118790 (e-PCR)
- UniSTS:138291

D3S3658 (e-PCR), detects polymorphism
- UniSTS:576

D5S1898 (e-PCR)
- UniSTS:16711

D5S1463 (e-PCR), detects polymorphism
- UniSTS:20575

SHGC-82576 (e-PCR)
- UniSTS:100711

G17003 (e-PCR)
- UniSTS:67433

SHGC-86171 (e-PCR)
- UniSTS:104812

D3S1578 (e-PCR)
- UniSTS:48238

GPR98 (e-PCR)
- UniSTS:504945

D5S1832E (e-PCR)
- UniSTS:153752

D5S428 (e-PCR), detects polymorphism
- UniSTS:23972

SHGC-154422 (e-PCR)
- UniSTS:178094

L28341 (e-PCR)
- UniSTS:50866

D5S484 (e-PCR)
- UniSTS:18359

G65490 (e-PCR)
- UniSTS:166590

RH119209 (e-PCR)
- UniSTS:138718

D5S433 (e-PCR), detects polymorphism
- UniSTS:74481

Genotypes

See GPR98 SNP Geneview Report
See GPR98 SNP Genotype Report
See GPR98 SNP Variation Viewer Report

Homology

Homologs of the GPR98 gene: The GPR98 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, and zebrafish.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Clone Names

KIAA0686, DKFZp761P0710

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
G-protein coupled receptor activity	NAS Non-traceable Author Statement more info	PubMed
calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
myosin binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info

Process	Evidence Code	Pubs
G-protein coupled receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
cell-cell adhesion	NAS Non-traceable Author Statement more info	PubMed
detection of mechanical stimulus involved in sensory perception of sound	IEA Inferred from Electronic Annotation more info
inner ear receptor stereocilium organization	IEA Inferred from Electronic Annotation more info
maintenance of organ identity	IMP Inferred from Mutant Phenotype more info	PubMed
nervous system development	NAS Non-traceable Author Statement more info	PubMed
neurological system process	IMP Inferred from Mutant Phenotype more info	PubMed
neuropeptide signaling pathway	IEA Inferred from Electronic Annotation more info
photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
sensory perception of light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
cell surface	IDA Inferred from Direct Assay more info	PubMed
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
integral to membrane	IEA Inferred from Electronic Annotation more info
membrane	NAS Non-traceable Author Statement more info	PubMed
plasma membrane	IEA Inferred from Electronic Annotation more info
stereocilia ankle link complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: G-protein coupled receptor 98

Names: G-protein coupled receptor 98; usher syndrome type-2C protein; very large G protein-coupled receptor 1; very large G-protein coupled receptor 1; monogenic, audiogenic seizure susceptibility 1 homolog; monogenic audiogenic seizure susceptibility protein 1 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007083.1 RefSeqGene

Range

5001..610417

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_032119.3 → NP_115495.3 G-protein coupled receptor 98 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as VLGR1b, encodes the predominant isoform (1).

Source sequence(s)

AC027323, AC034215, AC074132, AC093281, AC093529, AC094109, AC099512

Consensus CDS

CCDS47246.1

UniProtKB/Swiss-Prot

Q8WXG9

Related

ENSP00000384582, OTTHUMP00000222494, ENST00000405460, OTTHUMT00000369993

Conserved Domains (7) summary

pfam03736
Location:3396 – 3439
Blast Score: 107

EPTP; EPTP domain

smart00237
Location:4267 – 4354
Blast Score: 178

Calx_beta; Domains in Na-Ca exchangers and integrin-beta4

pfam01825
Location:5853 – 5895
Blast Score: 126

GPS; Latrophilin/CL-1-like GPS domain

pfam03160
Location:1728 – 1808
Blast Score: 175

Calx-beta; Calx-beta domain

pfam13385
Location:1346 – 1495
Blast Score: 178

Laminin_G_3; Concanavalin A-like lectin/glucanases superfamily

cl02522
Location:1977 – 2079
Blast Score: 148

Calx-beta; Calx-beta domain

cl12142
Location:5915 – 6148
Blast Score: 154

7tm_2; 7 transmembrane receptor (Secretin family)

RNA

NR_003149.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2), also known as VLGR1c, uses an alternate splice site in the 5' coding region, compared to variant 1. A CDS is not annotated because the transcript is a nonsense-mediated mRNA decay (NMD) candidate.

Source sequence(s)

AC027323, AC034215, AC074132, AC093281, AC093529, AC094109, AC099512

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000005.9 Reference GRCh37.p10 Primary Assembly

Range

89854617..90460033

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000137.1 Alternate HuRef

Range

85065303..85671984

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018916.1 Alternate CHM1_1.0

Range

90135839..90741012

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01062155.1 (50820..86724)	None
genomic	ABBA01062156.1	None
genomic	ABBA01062157.1	None
genomic	ABBA01062158.1	None
genomic	ABBA01062159.1	None
genomic	ABBA01062160.1	None
genomic	ABBA01062161.1	None
genomic	ABBA01062162.1	None
genomic	AC027323.5	None
genomic	AC034215.4 (34262..126030)	None
genomic	AC074132.5 (375..118131)	None
genomic	AC093281.2 (44499..65538)	None
genomic	AC093529.2	None
genomic	AC094109.2	None
genomic	AC099512.2	None
genomic	AMYH01015478.1 (65083..101190)	None
genomic	AMYH01015479.1	None
genomic	AMYH01015480.1	None
genomic	CH471084.1	EAW95986.1
		EAW95987.1
		EAW95988.1
		EAW95989.1
		EAW95990.1
		EAW95991.1
		EAW95992.1
		EAW95993.1
		EAW95994.1
mRNA	AB014586.2	BAA31661.2
mRNA	AB075823.1	BAB85529.1
mRNA	AF055084.1	AAD55586.1
mRNA	AF435925.1	AAL30811.1
mRNA	AK024416.1	BAG51297.1
mRNA	AL133041.1	CAB61369.2
mRNA	AL136541.1	CAB66476.2
mRNA	BC034748.1	None
mRNA	BI758469.1	None
mRNA	BX493741.1	None
mRNA	CD633594.1	None
mRNA	DA503892.1	None