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OPHN1 oligophrenin 1 [ Homo sapiens (human) ]

Gene ID: 4983, updated on 1-Jun-2020

Summary

Official Symbol
OPHN1provided by HGNC
Official Full Name
oligophrenin 1provided by HGNC
Primary source
HGNC:HGNC:8148
See related
Ensembl:ENSG00000079482 MIM:300127
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
OPN1; MRX60; ARHGAP41
Summary
This gene encodes a Rho-GTPase-activating protein that promotes GTP hydrolysis of Rho subfamily members. Rho proteins are important mediators of intracellular signal transduction, which affects cell migration and cell morphogenesis. Mutations in this gene are responsible for OPHN1-related X-linked cognitive disability with cerebellar hypoplasia and distinctive facial dysmorhphism. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 5.5), prostate (RPKM 3.3) and 21 other tissues See more
Orthologs

Genomic context

See OPHN1 in Genome Data Viewer
Location:
Xq12
Exon count:
27
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (68042344..68433841, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (67262186..67653369, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373241 Neighboring gene Sharpr-MPRA regulatory region 14511 Neighboring gene BMI1 proto-oncogene, polycomb ring finger pseudogene 1 Neighboring gene RNA, U6 small nuclear 1225, pseudogene Neighboring gene phosphoglycerate kinase 1 pseudogene 1 Neighboring gene akirin 1 pseudogene 2 Neighboring gene nuclear distribution protein nudE-like 1-like Neighboring gene RNA, U6 small nuclear 245, pseudogene Neighboring gene Yip1 domain family member 6

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation X-linked with cerebellar hypoplasia and distinctive facial appearance
MedGen: C1845366 OMIM: 300486 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-07-27)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-27)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
actin binding IEA
Inferred from Electronic Annotation
more info
 
ionotropic glutamate receptor binding IEA
Inferred from Electronic Annotation
more info
 
phospholipid binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon guidance TAS
Traceable Author Statement
more info
PubMed 
cell junction assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell morphogenesis involved in neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cerebellar granule cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cerebral cortex neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
establishment of epithelial cell apical/basal polarity IMP
Inferred from Mutant Phenotype
more info
PubMed 
maintenance of postsynaptic specialization structure IEA
Inferred from Electronic Annotation
more info
 
negative regulation of proteasomal protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron projection development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
regulation of Rho protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of postsynaptic neurotransmitter receptor internalization EXP
Inferred from Experiment
more info
PubMed 
regulation of postsynaptic neurotransmitter receptor internalization IDA
Inferred from Direct Assay
more info
PubMed 
regulation of postsynaptic neurotransmitter receptor internalization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of small GTPase mediated signal transduction TAS
Traceable Author Statement
more info
 
regulation of synaptic transmission, glutamatergic IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
substrate-dependent cell migration, cell extension TAS
Traceable Author Statement
more info
PubMed 
synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
dendritic spine IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glutamatergic synapse EXP
Inferred from Experiment
more info
PubMed 
glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
terminal bouton IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
oligophrenin-1
Names
mental retardation, X-linked 60
oligophrenin-1, Rho-GTPase activating protein

NCBI Reference Sequences (RefSeq)

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

  1. NG_008960.1 RefSeqGene

    Range
    4963..396114
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002547.3NP_002538.1  oligophrenin-1

    See identical proteins and their annotated locations for NP_002538.1

    Status: REVIEWED

    Source sequence(s)
    AJ001189, AL157700, AL672138, BP357826
    Consensus CDS
    CCDS14388.1
    UniProtKB/Swiss-Prot
    O60890
    Related
    ENSP00000347710.5, ENST00000355520.6
    Conserved Domains (4) summary
    cd07633
    Location:19225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363559
    RhoGAP_Graf; RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences ...
    cd01249
    Location:267370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain
    pfam00169
    Location:266363
    PH; PH domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    68042344..68433841 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530961.1XP_011529263.1  oligophrenin-1 isoform X1

    See identical proteins and their annotated locations for XP_011529263.1

    UniProtKB/Swiss-Prot
    O60890
    Conserved Domains (4) summary
    cd07633
    Location:19225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363559
    RhoGAP_Graf; RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences ...
    cd01249
    Location:267370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain
    pfam00169
    Location:266363
    PH; PH domain
  2. XM_005262270.1XP_005262327.1  oligophrenin-1 isoform X3

    See identical proteins and their annotated locations for XP_005262327.1

    Conserved Domains (3) summary
    cd07633
    Location:19225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363559
    RhoGAP_Graf; RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences ...
    cd01249
    Location:267370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain
  3. XM_006724653.2XP_006724716.1  oligophrenin-1 isoform X2

    Conserved Domains (4) summary
    cd07633
    Location:19225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363559
    RhoGAP_Graf; RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences ...
    cd01249
    Location:267370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain
    pfam00169
    Location:266363
    PH; PH domain
  4. XM_017029555.1XP_016885044.1  oligophrenin-1 isoform X4

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