Human Gene GPR98 (uc003kju.3) Description and Page Index
  Description: Homo sapiens G protein-coupled receptor 98 (GPR98), transcript variant 1, mRNA.
RefSeq Summary (NM_032119): 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]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AF435925.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN03267750, SAMN03267768 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000405460.9/ ENSP00000384582.2 RefSeq Select criteria :: based on conservation ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr5:89,854,617-90,460,033 Size: 605,417 Total Exon Count: 90 Strand: +
Coding Region
   Position: hg19 chr5:89,854,713-90,459,717 Size: 605,005 Coding Exon Count: 90 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:89,854,617-90,460,033)mRNA (may differ from genome)Protein (6306 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDHuman Cortex Gene ExpressionLynx
MGIneXtProtOMIMPubMedStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: GPR98_HUMAN
DESCRIPTION: RecName: Full=G-protein coupled receptor 98; AltName: Full=Monogenic audiogenic seizure susceptibility protein 1 homolog; AltName: Full=Usher syndrome type-2C protein; AltName: Full=Very large G-protein coupled receptor 1; Flags: Precursor;
FUNCTION: Receptor that may have an important role in the development of the central nervous system.
SUBUNIT: Interacts with WHRN. Interacts with PDZD7.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed at low levels in adult tissues.
DEVELOPMENTAL STAGE: Isoform 1 is 4 times more abundant than isoform 2 in most tissues tested, despite wide variations in absolute levels of expression. Isoform 3 is expressed at about 1.5 times isoform 1 levels in most tissues examined. In fetal testis, isoform 3 is expressed almost exclusively.
DISEASE: Defects in GPR98 are the cause of Usher syndrome type 2C (USH2C) [MIM:605472]. USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses.
DISEASE: Defects in GPR98 may be a cause of familial febrile convulsions type 4 (FEB4) [MIM:604352]; also known as familial febrile seizures 4. Febrile convulsions are seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy.
MISCELLANEOUS: By far is the largest known cell surface protein.
SIMILARITY: Belongs to the G-protein coupled receptor 2 family. LN-TM7 subfamily.
SIMILARITY: Contains 35 Calx-beta domains.
SIMILARITY: Contains 6 EAR repeats.
SIMILARITY: Contains 1 GPS domain.
SEQUENCE CAUTION: Sequence=AAL30811.1; Type=Frameshift; Positions=3524, 3532; Sequence=CAB66476.2; Type=Erroneous translation; Note=Wrong genetic code use for translating the sequence;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/GPR98";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GPR98
CDC HuGE Published Literature: GPR98
Positive Disease Associations: Benzodiazepines , Body Weight , Bone Density , Calcium , Carotid Artery Diseases , Carotid Stenosis , Coronary Artery Disease , Hip , hip geometry , response to antipsychotic treatment
Related Studies:
  1. Benzodiazepines
    D E Adkins et al. Molecular psychiatry 2011, Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs., Molecular psychiatry. [PubMed 20195266]
  2. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Bone Density
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.
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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.00 RPKM in Adrenal Gland
Total median expression: 80.39 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.9096-0.332 Picture PostScript Text
3' UTR -65.70316-0.208 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003644 - Calx_beta
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR009039 - EAR
IPR005492 - EPTP
IPR017981 - GPCR_2-like
IPR000832 - GPCR_2_secretin-like
IPR000203 - GPS_dom

Pfam Domains:
PF00002 - 7 transmembrane receptor (Secretin family)
PF03160 - Calx-beta domain
PF03736 - EPTP domain
PF13385 - Concanavalin A-like lectin/glucanases superfamily

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases

ModBase Predicted Comparative 3D Structure on Q8WXG9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0004888 transmembrane signaling receptor activity
GO:0004930 G-protein coupled receptor activity
GO:0005509 calcium ion binding
GO:0005515 protein binding

Biological Process:
GO:0007154 cell communication
GO:0007165 signal transduction
GO:0007166 cell surface receptor signaling pathway
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007399 nervous system development
GO:0007601 visual perception
GO:0007605 sensory perception of sound
GO:0045494 photoreceptor cell maintenance
GO:0048496 maintenance of animal organ identity
GO:0050877 neurological system process
GO:0050896 response to stimulus
GO:0050953 sensory perception of light stimulus
GO:0098609 cell-cell adhesion

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032420 stereocilium
GO:0043235 receptor complex
GO:0045202 synapse
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF435925 - Homo sapiens very large G protein-coupled receptor 1b (VLGR1) mRNA, complete cds.
AF055084 - Homo sapiens very large G-protein coupled receptor-1 (VLGR1) mRNA, complete cds.
AK024416 - Homo sapiens cDNA FLJ14354 fis, clone Y79AA1001384, highly similar to Monogenic audiogenic seizure susceptibility protein 1 homolog precursor.
AB014586 - Homo sapiens mRNA for KIAA0686 protein, partial cds.
BC172212 - Synthetic construct Homo sapiens clone IMAGE:9094358 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
BC172199 - Synthetic construct Homo sapiens clone IMAGE:9094289 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
BC172219 - Synthetic construct Homo sapiens clone IMAGE:9094300 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
AL136541 - Homo sapiens mRNA; cDNA DKFZp761P0710 (from clone DKFZp761P0710).
BC172210 - Synthetic construct Homo sapiens clone IMAGE:9094354 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
BC034748 - Homo sapiens G protein-coupled receptor 98, mRNA (cDNA clone IMAGE:5183306), with apparent retained intron.
JD206042 - Sequence 187066 from Patent EP1572962.
BC172200 - Synthetic construct Homo sapiens clone IMAGE:9094290 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
AB075823 - Homo sapiens mRNA for KIAA1943 protein.
AL133041 - Homo sapiens mRNA; cDNA DKFZp434L2050 (from clone DKFZp434L2050).
BC172211 - Synthetic construct Homo sapiens clone IMAGE:9094356 G protein-coupled receptor 98 precursor (GPR98) gene, partial cds.
JD288327 - Sequence 269351 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: GPR98_HUMAN, KIAA0686, KIAA1943, MASS1, NM_032119, NP_115495, O75171, Q8TF58, Q8WXG9, Q9H0X5, Q9UL61, VLGR1
UCSC ID: uc003kju.3
RefSeq Accession: NM_032119
Protein: Q8WXG9 (aka GPR98_HUMAN)
CCDS: CCDS47246.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032119.3
exon count: 90CDS single in 3' UTR: no RNA size: 19333
ORF size: 18921CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 33541.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.