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 dysmorhphi... See more...

Aliases for OPHN1 Gene

Aliases for OPHN1 Gene

  • Oligophrenin 1 2 3 5
  • Mental Retardation, X-Linked 60 2 3
  • Oligophrenin-1 3 4
  • Oligophrenin-1, Rho-GTPase Activating Protein 3
  • ARHGAP41 3
  • MRX60 3
  • OPN1 3

External Ids for OPHN1 Gene

Previous HGNC Symbols for OPHN1 Gene

  • MRX60

Previous GeneCards Identifiers for OPHN1 Gene

  • GC0XM063483
  • GC0XM064728
  • GC0XM065495
  • GC0XM066129
  • GC0XM067045
  • GC0XM067178
  • GC0XM061092
  • GC0XM067262

Summaries for OPHN1 Gene

Entrez Gene Summary for OPHN1 Gene

  • 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]

GeneCards Summary for OPHN1 Gene

OPHN1 (Oligophrenin 1) is a Protein Coding gene. Diseases associated with OPHN1 include Mental Retardation, X-Linked, With Cerebellar Hypoplasia And Distinctive Facial Appearance and Cerebellar Hypoplasia. Among its related pathways are Signaling by GPCR and Signaling by Rho GTPases. Gene Ontology (GO) annotations related to this gene include actin binding and phospholipid binding. An important paralog of this gene is ARHGAP42.

UniProtKB/Swiss-Prot Summary for OPHN1 Gene

  • Stimulates GTP hydrolysis of members of the Rho family. Its action on RHOA activity and signaling is implicated in growth and stabilization of dendritic spines, and therefore in synaptic function. Critical for the stabilization of AMPA receptors at postsynaptic sites. Critical for the regulation of synaptic vesicle endocytosis at presynaptic terminals. Required for the localization of NR1D1 to dendrites, can suppress its repressor activity and protect it from proteasomal degradation (By similarity).

Gene Wiki entry for OPHN1 Gene

Additional gene information for OPHN1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for OPHN1 Gene

Genomics for OPHN1 Gene

GeneHancer (GH) Regulatory Elements for OPHN1 Gene

Promoters and enhancers for OPHN1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ068432 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.7 661 3.3 ZNF217 NRF1 POLR2G ZIC2 POLR2A ZBTB10 ZBTB11 ZNF423 ZBTB26 REST OPHN1 lnc-OPHN1-2 RF00017-8488 RF00017-8485
GH0XJ068454 Enhancer 0.7 Ensembl ENCODE 13.8 -21.0 -21029 0.9 TCF12 FOXA2 JUND GATA3 FOXP1 FOXA1 DPF2 TCF7L2 ELF3 SMARCE1 OPHN1 YIPF6 piR-43107-317 lnc-OPHN1-2 RF00017-8485
GH0XJ068411 Enhancer 0.5 Ensembl 14 +21.6 21613 0.6 ZNF217 CTBP1 DPF2 PRDM6 GATA3 SMARCE1 OPHN1 RF00017-8488 ENSG00000206646 RF00017-8485
GH0XJ069094 Enhancer 0.5 Ensembl 11.2 -660.3 -660324 0.7 CTCF REST SALL2 SMC3 ZFHX2 RAD21 ZSCAN26 EGR2 ZNF473 ZNF143 PJA1 OPHN1 LOC105373242 HSALNG0138377
GH0XJ068480 Enhancer 0.3 Ensembl 13.3 -47.1 -47088 0.8 CEBPB ZNF512 piR-49423-294 OPHN1 RF00017-8485
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around OPHN1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for OPHN1

Top Transcription factor binding sites by QIAGEN in the OPHN1 gene promoter:
  • GATA-1
  • GATA-2
  • GATA-3
  • IRF-7A
  • Lmo2
  • MyoD
  • NF-AT
  • NF-AT1
  • NF-AT2
  • Nkx2-5

Genomic Locations for OPHN1 Gene

Genomic Locations for OPHN1 Gene
chrX:68,042,344-68,433,913
(GRCh38/hg38)
Size:
391,570 bases
Orientation:
Minus strand
chrX:67,262,186-67,653,755
(GRCh37/hg19)
Size:
391,570 bases
Orientation:
Minus strand

Genomic View for OPHN1 Gene

Genes around OPHN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
OPHN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for OPHN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for OPHN1 Gene

Proteins for OPHN1 Gene

  • Protein details for OPHN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60890-OPHN1_HUMAN
    Recommended name:
    Oligophrenin-1
    Protein Accession:
    O60890
    Secondary Accessions:
    • B9EIP8
    • Q5JQ81
    • Q6PCC1
    • Q8WX47

    Protein attributes for OPHN1 Gene

    Size:
    802 amino acids
    Molecular mass:
    91641 Da
    Quaternary structure:
    • Interacts with HOMER1. Interacts with AMPA receptor complexes. Interacts with SH3GL2 (endophilin-A1) (By similarity). Interacts (via C-terminus) with NR1D1 (By similarity).

    Alternative splice isoforms for OPHN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for OPHN1 Gene

Post-translational modifications for OPHN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for OPHN1 Gene

No data available for DME Specific Peptides for OPHN1 Gene

Domains & Families for OPHN1 Gene

Gene Families for OPHN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for OPHN1 Gene

Blocks:
  • RhoGAP domain
  • Pleckstrin-like
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for OPHN1 Gene

GenScript: Design optimal peptide antigens:
  • Oligophrenin-1 (OPHN1_HUMAN)
  • OPHN1 protein (Q6PCC1_HUMAN)
  • Oligophrenin 1 (Q7Z2H1_HUMAN)
genes like me logo Genes that share domains with OPHN1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for OPHN1 Gene

Function for OPHN1 Gene

Molecular function for OPHN1 Gene

UniProtKB/Swiss-Prot Function:
Stimulates GTP hydrolysis of members of the Rho family. Its action on RHOA activity and signaling is implicated in growth and stabilization of dendritic spines, and therefore in synaptic function. Critical for the stabilization of AMPA receptors at postsynaptic sites. Critical for the regulation of synaptic vesicle endocytosis at presynaptic terminals. Required for the localization of NR1D1 to dendrites, can suppress its repressor activity and protect it from proteasomal degradation (By similarity).

Phenotypes From GWAS Catalog for OPHN1 Gene

Gene Ontology (GO) - Molecular Function for OPHN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005096 GTPase activator activity IBA,TAS 21873635
GO:0005543 phospholipid binding IDA 18954304
GO:0035255 ionotropic glutamate receptor binding IEA --
genes like me logo Genes that share ontologies with OPHN1: view
genes like me logo Genes that share phenotypes with OPHN1: view

Human Phenotype Ontology for OPHN1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for OPHN1 Gene

MGI Knock Outs for OPHN1:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for OPHN1 Gene

Localization for OPHN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for OPHN1 Gene

Cell junction, synapse, postsynapse. Cell junction, synapse, presynapse. Cell projection, axon. Cell projection, dendritic spine. Cell projection, dendrite. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for OPHN1 gene
Compartment Confidence
cytosol 5
cytoskeleton 4
plasma membrane 3
nucleus 3
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for OPHN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol TAS --
GO:0015629 actin cytoskeleton IBA,IEA 21873635
GO:0030054 cell junction IEA --
GO:0030424 axon IEA --
genes like me logo Genes that share ontologies with OPHN1: view

Pathways & Interactions for OPHN1 Gene

genes like me logo Genes that share pathways with OPHN1: view

Pathways by source for OPHN1 Gene

1 BioSystems pathway for OPHN1 Gene
1 Cell Signaling Technology pathway for OPHN1 Gene

Gene Ontology (GO) - Biological Process for OPHN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis IEA --
GO:0006930 substrate-dependent cell migration, cell extension TAS 9582072
GO:0007165 signal transduction TAS,IEA --
GO:0007399 nervous system development TAS 9582072
GO:0007411 axon guidance TAS 9582072
genes like me logo Genes that share ontologies with OPHN1: view

No data available for SIGNOR curated interactions for OPHN1 Gene

Drugs & Compounds for OPHN1 Gene

(1) Drugs for OPHN1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with OPHN1: view

Transcripts for OPHN1 Gene

mRNA/cDNA for OPHN1 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for OPHN1 Gene

No ASD Table

Relevant External Links for OPHN1 Gene

GeneLoc Exon Structure for
OPHN1

Expression for OPHN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for OPHN1 Gene

Protein differential expression in normal tissues from HIPED for OPHN1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (20.3), Breast (16.5), Placenta (7.6), and Fetal Brain (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for OPHN1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for OPHN1

SOURCE GeneReport for Unigene cluster for OPHN1 Gene:

Hs.128824

mRNA Expression by UniProt/SwissProt for OPHN1 Gene:

O60890-OPHN1_HUMAN
Tissue specificity: Expressed in brain.

Evidence on tissue expression from TISSUES for OPHN1 Gene

  • Nervous system(4.5)
  • Lung(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for OPHN1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • nose
  • outer ear
  • skull
  • tooth
Pelvis:
  • penis
  • testicle
Limb:
  • lower limb
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with OPHN1: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for OPHN1 Gene

Orthologs for OPHN1 Gene

This gene was present in the common ancestor of animals.

Orthologs for OPHN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia OPHN1 31 30
  • 99.83 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LOC525644 30
  • 92.23 (n)
dog
(Canis familiaris)
Mammalia OPHN1 31 30
  • 92.18 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia OPHN1 31
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ophn1 17 31 30
  • 88.03 (n)
rat
(Rattus norvegicus)
Mammalia Ophn1 30
  • 87.12 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia OPHN1 31
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves OPHN1 31 30
  • 79.1 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia OPHN1 31
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ophn1 30
  • 68.86 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC68856 30
zebrafish
(Danio rerio)
Actinopterygii ophn1 31
  • 63 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Graf 31 32
  • 27 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T04C9.1 31
  • 29 (a)
OneToMany
Species where no ortholog for OPHN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for OPHN1 Gene

ENSEMBL:
Gene Tree for OPHN1 (if available)
TreeFam:
Gene Tree for OPHN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for OPHN1: view image

Paralogs for OPHN1 Gene

Paralogs for OPHN1 Gene

(16) SIMAP similar genes for OPHN1 Gene using alignment to 4 proteins:

  • OPHN1_HUMAN
  • F5H2E3_HUMAN
  • Q6PCC1_HUMAN
  • Q7Z2H1_HUMAN

Pseudogenes.org Pseudogenes for OPHN1 Gene

genes like me logo Genes that share paralogs with OPHN1: view

Variants for OPHN1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for OPHN1 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
636256 Likely Pathogenic: Mental retardation X-linked with cerebellar hypoplasia and distinctive facial appearance 68,119,248(-) C/T MISSENSE_VARIANT
663708 Uncertain Significance: not provided 68,193,952(-) A/G MISSENSE_VARIANT
667769 Benign: not provided 68,432,671(-) A/G INTRON_VARIANT
667771 Benign: not provided 68,212,457(-) C/T INTRON_VARIANT
667774 Benign: not provided 68,211,972(-) A/G INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for OPHN1 Gene

Structural Variations from Database of Genomic Variants (DGV) for OPHN1 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER inversion 17803354
esv2575463 CNV deletion 19546169
esv2676108 CNV deletion 23128226
esv2740203 CNV deletion 23290073
esv2758871 CNV gain 17122850
esv3362712 CNV insertion 20981092
esv3574019 CNV loss 25503493
esv3574021 CNV loss 25503493
nsv436640 CNV deletion 17901297
nsv517446 CNV gain 19592680
nsv6938 CNV deletion 18451855
nsv6939 CNV deletion 18451855
nsv818030 CNV gain 17921354

Variation tolerance for OPHN1 Gene

Residual Variation Intolerance Score: 50.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.88; 48.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for OPHN1 Gene

Human Gene Mutation Database (HGMD)
OPHN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
OPHN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for OPHN1 Gene

Disorders for OPHN1 Gene

MalaCards: The human disease database

(14) MalaCards diseases for OPHN1 Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search OPHN1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

OPHN1_HUMAN
  • Mental retardation, X-linked, syndromic, OPHN1-related (MRXSO) [MIM:300486]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXSO patients manifest mental retardation associated with cerebellar hypoplasia and distinctive facial dysmorphism. {ECO:0000269 PubMed:10439959, ECO:0000269 PubMed:21796728, ECO:0000269 PubMed:9582072}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for OPHN1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with OPHN1: view

No data available for Genatlas for OPHN1 Gene

Publications for OPHN1 Gene

  1. Oligophrenin-1 encodes a rhoGAP protein involved in X-linked mental retardation. (PMID: 9582072) Billuart P … Chelly J (Nature 1998) 2 3 4 23 54
  2. [Anassociation study between OPHN1 gene rs492933 polymorphism and mental retardation in children of the Qinba Mountain region.]. (PMID: 18930891) Zhang LJ … Zhang FC (Yi chuan = Hereditas 2008) 3 23 41 54
  3. Oligophrenin 1 mutations frequently cause X-linked mental retardation with cerebellar hypoplasia. (PMID: 16221952) Zanni G … Chelly J (Neurology 2005) 3 23 41 54
  4. Determination of the gene structure of human oligophrenin-1 and identification of three novel polymorphisms by screening of DNA from 164 patients with non-specific X-linked mental retardation. (PMID: 10818214) Billuart P … Bienvenu T (Annales de genetique 2000) 3 4 23 54
  5. Deletion including the oligophrenin-1 gene associated with enlarged cerebral ventricles, cerebellar hypoplasia, seizures and ataxia. (PMID: 10439959) Tentler D … Dahl N (European journal of human genetics : EJHG 1999) 3 4 23 54

Products for OPHN1 Gene

Sources for OPHN1 Gene