OPHN1 oligophrenin 1 [Homo sapiens (human)] - Gene

Summary

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

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Androgen deprivationinduced OPHN1 amplification promotes castrationresistant prostate cancer.
Title: Androgen deprivation‑induced OPHN1 amplification promotes castration‑resistant prostate cancer.
Novel unconventional variants expand the allelic spectrum of OPHN1 gene.
Title: Novel unconventional variants expand the allelic spectrum of OPHN1 gene.
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.
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.
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.
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.
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.
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.
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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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	not available

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G64121 (e-PCR)
- UniSTS:146694

G64120 (e-PCR)
- UniSTS:146698

G64126 (e-PCR)
- UniSTS:146699

G64127 (e-PCR)
- UniSTS:146705

DXS7497 (e-PCR)
- UniSTS:29995

D11S3017 (e-PCR)
- UniSTS:152121

DYS416 (e-PCR)
- UniSTS:38201

G64125 (e-PCR)
- UniSTS:146748

G64123 (e-PCR)
- UniSTS:146749

WI-12732 (e-PCR)
- UniSTS:19261

G64122 (e-PCR)
- UniSTS:146750

RH10979 (e-PCR)
- UniSTS:51266

RH67878 (e-PCR)
- UniSTS:58446

RH120295 (e-PCR)
- UniSTS:132437

RH64534 (e-PCR)
- UniSTS:91990

DXS2493 (e-PCR)
- UniSTS:14690

RH36157 (e-PCR)
- UniSTS:26729

PGK1P1 (e-PCR)
- UniSTS:99699

DXS897 (e-PCR)
- UniSTS:98940

D11S3114 (e-PCR)
- UniSTS:152207

GDB:194746 (e-PCR)
- UniSTS:155802

DXS908 (e-PCR)
- UniSTS:99739

GDB:181567 (e-PCR)
- UniSTS:155292

L77752 (e-PCR)
- UniSTS:41119

D11S2766 (e-PCR)
- UniSTS:151969

RH79992 (e-PCR)
- UniSTS:86193

NoName (e-PCR)
- UniSTS:62643

DXS905 (e-PCR)
- UniSTS:99522

AL033784 (e-PCR)
- UniSTS:93636

A004A36 (e-PCR)
- UniSTS:17358

DXS896 (e-PCR)
- UniSTS:147153

DXS1160 (e-PCR)
- UniSTS:99292

WI-19211 (e-PCR)
- UniSTS:78070

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

NG_008960.1 RefSeqGene

Range

4963..396114

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

68042344..68433841 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
XM_047442144.1 → XP_047298100.1 oligophrenin-1 isoform X3
XM_047442145.1 → XP_047298101.1 oligophrenin-1 isoform X5
XM_017029555.2 → XP_016885044.1 oligophrenin-1 isoform X5

UniProtKB/TrEMBL

A0A7P0T8V5

Related

ENSP00000505365.1, ENST00000680612.1