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OPHN1 oligophrenin 1 [ Homo sapiens (human) ]

Gene ID: 4983, updated on 10-Dec-2024

Summary

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Official Symbol
OPHN1provided by HGNC
Official Full Name
oligophrenin 1provided by HGNC
Primary source
HGNC:HGNC:8148
See related
Ensembl:ENSG00000079482 MIM:300127; AllianceGenome:HGNC:8148
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; MRXSBL; 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
mouse all
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Genomic context

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See OPHN1 in Genome Data Viewer
Location:
Xq12
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (68042344..68433841, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (66475136..66867394, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (67262186..67653337, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14511 Neighboring gene negative expression of androgen receptor regulating lncRNA Neighboring gene BMI1 proto-oncogene, polycomb ring finger pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chrX:67280228-67280729 Neighboring gene RNA, U6 small nuclear 1225, pseudogene Neighboring gene phosphoglycerate kinase 1 pseudogene 1 Neighboring gene akirin 1 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:67575188-67575688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:67575689-67576189 Neighboring gene Sharpr-MPRA regulatory region 7273 Neighboring gene nuclear distribution protein nudE-like 1-like Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:67718059-67718733 Neighboring gene Yip1 domain family member 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Effect of the OPHN1 novel variant c.1025+1 G>A on RNA splicing: insights from a minigene assay. Yang F, et al. BMC Med Genomics, 2024 Jul 2. PMID 38956616, Free PMC Article
  2. Sporadic male patients with intellectual disability: contribution of X-chromosome copy number variants. Isrie M, et al. Eur J Med Genet, 2012 Nov. PMID 22659343
  3. [Anassociation study between OPHN1 gene rs492933 polymorphism and mental retardation in children of the Qinba Mountain region.]. Zhang LJ, et al. Yi Chuan, 2008 Oct. PMID 18930891
  4. Association of syndromic mental retardation with an Xq12q13.1 duplication encompassing the oligophrenin 1 gene. Bedeschi MF, et al. Am J Med Genet A, 2008 Jul 1. PMID 18512229
  5. Oligophrenin-1 (OPHN1), a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development. Barresi S, et al. PLoS One, 2014. PMID 24637888, Free PMC Article

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Effect of the OPHN1 novel variant c.1025+1 G>A on RNA splicing: insights from a minigene assay.
    Title: Effect of the OPHN1 novel variant c.1025+1 G>A on RNA splicing: insights from a minigene assay.
  2. Androgen deprivationinduced OPHN1 amplification promotes castrationresistant prostate cancer.
    Title: Androgen deprivation‑induced OPHN1 amplification promotes castration‑resistant prostate cancer.
  3. Novel unconventional variants expand the allelic spectrum of OPHN1 gene.
    Title: Novel unconventional variants expand the allelic spectrum of OPHN1 gene.
  4. Here, we report that chronic treatment in adult mouse with Fasudil, is able to counteract vertical and horizontal hyperactivities, restores recognition memory and limits the brain ventricular dilatation observed in Ophn1(-)(/y) However, deficits in working and spatial memories are partially or not rescued by the treatment
    Title: Fasudil treatment in adult reverses behavioural changes and brain ventricular enlargement in Oligophrenin-1 mouse model of intellectual disability.
  5. Furthermore, we found that olfactory behaviour was perturbed in OPHN1 ko mice. Chronic treatment with a Rho kinase inhibitor rescued most of the defects of the newly generated neurons. Altogether, our data indicated that OPHN1 plays a key role in regulating the number, morphology and function of adult-born inhibitory interneurons and contributed to identify potential therapeutic targets.
    Title: Oligophrenin-1 regulates number, morphology and synaptic properties of adult-born inhibitory interneurons in the olfactory bulb.
  6. we reported on the first male patient carrying an OPHN1 mutation with IQ score within the normal limits. This observation expands the phenotypic spectrum of OPHN1 mutations.
    Title: Large in-frame intragenic deletion of OPHN1 in a male patient with a normal intelligence quotient score.
  7. A neuronal stem cell-based model for the treatment of OPHN1 syndrome and other neurological disorders due to ROCK dysfunction.
    Title: Rho Kinase Inhibition Is Essential During In Vitro Neurogenesis and Promotes Phenotypic Rescue of Human Induced Pluripotent Stem Cell-Derived Neurons With Oligophrenin-1 Loss of Function.
  8. results suggest that oligophrenin-1 is involved in tumor progression in prostate cancer
    Title: Oligophrenin-1 is associated with cell adhesion and migration in prostate cancer.
  9. This is the first description of an in-frame deletion within the BAR domain of OPHN1 and could provide new insights into the role of this domain in relation to brain and cognitive development or function.
    Title: A novel in-frame deletion affecting the BAR domain of OPHN1 in a family with intellectual disability and hippocampal alterations.
  10. Our results demonstrate that multiple post-transcriptional events occur on OPHN1, a gene playing an important role in brain function and development.
    Title: Oligophrenin-1 (OPHN1), a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development.
Submit: New GeneRIF Correction See all GeneRIFs (21)

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

Associated conditions

Description Tests
X-linked intellectual disability-cerebellar hypoplasia syndrome
MedGen: C1845366 OMIM: 300486 GeneReviews: Not available
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Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2023-03-22)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2023-03-22)

ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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Preferred Names
oligophrenin-1
Names
oligophrenin-1, Rho-GTPase activating protein

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

  1. NG_008960.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_002547.3 → NP_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
    B9EIP8, O60890, Q5JQ81, Q6PCC1, Q8WX47
    UniProtKB/TrEMBL
    A0A7P0TBH4
    Related
    ENSP00000347710.5, ENST00000355520.6
    Conserved Domains (4) summary
    cd07633
    Location:19 → 225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363 → 559
    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:267 → 370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain
    pfam00169
    Location:266 → 363
    PH; PH domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011530961.2 → XP_011529263.1  oligophrenin-1 isoform X1

    See identical proteins and their annotated locations for XP_011529263.1

    UniProtKB/Swiss-Prot
    B9EIP8, O60890, Q5JQ81, Q6PCC1, Q8WX47
    UniProtKB/TrEMBL
    A0A7P0TBH4
    Conserved Domains (4) summary
    cd07633
    Location:19 → 225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363 → 559
    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:267 → 370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain
    pfam00169
    Location:266 → 363
    PH; PH domain

  2. XM_005262270.2 → XP_005262327.1  oligophrenin-1 isoform X4

    See identical proteins and their annotated locations for XP_005262327.1

    UniProtKB/TrEMBL
    A0A7P0Z4E9, B4DIT2
    Related
    ENSP00000505800.1, ENST00000679748.1
    Conserved Domains (3) summary
    cd07633
    Location:19 → 225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363 → 559
    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 cytoskeletal ...
    cd01249
    Location:267 → 370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain

  3. XM_006724653.3 → XP_006724716.1  oligophrenin-1 isoform X2

    UniProtKB/TrEMBL
    A0A7P0TBH4
    Conserved Domains (4) summary
    cd07633
    Location:19 → 225
    BAR_OPHN1; The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1
    cd04374
    Location:363 → 559
    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:267 → 370
    BAR-PH_GRAF_family; GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain
    pfam00169
    Location:266 → 363
    PH; PH domain

  4. XM_047442144.1 → XP_047298100.1  oligophrenin-1 isoform X3

    UniProtKB/TrEMBL
    A0A7P0TBH4

  5. XM_047442145.1 → XP_047298101.1  oligophrenin-1 isoform X5

    UniProtKB/TrEMBL
    A0A7P0T8V5

  6. XM_017029555.2 → XP_016885044.1  oligophrenin-1 isoform X5

    UniProtKB/TrEMBL
    A0A7P0T8V5
    Related
    ENSP00000505365.1, ENST00000680612.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    66475136..66867394 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327139.1 → XP_054183114.1  oligophrenin-1 isoform X1

    UniProtKB/TrEMBL
    A0A7P0TBH4

  2. XM_054327142.1 → XP_054183117.1  oligophrenin-1 isoform X4

    UniProtKB/TrEMBL
    B4DIT2

  3. XM_054327140.1 → XP_054183115.1  oligophrenin-1 isoform X2

    UniProtKB/TrEMBL
    A0A7P0TBH4

  4. XM_054327141.1 → XP_054183116.1  oligophrenin-1 isoform X3

    UniProtKB/TrEMBL
    A0A7P0TBH4

  5. XM_054327144.1 → XP_054183119.1  oligophrenin-1 isoform X5

    UniProtKB/TrEMBL
    A0A7P0T8V5

  6. XM_054327143.1 → XP_054183118.1  oligophrenin-1 isoform X5

    UniProtKB/TrEMBL
    A0A7P0T8V5
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60890.1 GenPept UniProtKB/Swiss-Prot:O60890

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