Human Gene OPHN1 (ENST00000355520.6_7) from GENCODE V47lift37
  Description: oligophrenin 1 (from RefSeq NM_002547.3)
Gencode Transcript: ENST00000355520.6_7
Gencode Gene: ENSG00000079482.14_11
Transcript (Including UTRs)
   Position: hg19 chrX:67,262,186-67,653,337 Size: 391,152 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg19 chrX:67,268,266-67,652,862 Size: 384,597 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:67,262,186-67,653,337)mRNA (may differ from genome)Protein (802 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: OPHN1_HUMAN
DESCRIPTION: RecName: Full=Oligophrenin-1;
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 (By similarity). Critical for the stabilization of AMPA receptors at postsynaptic sites (By similarity). Critical for the regulation of synaptic vesicle endocytosis at presynaptic terminals (By similarity).
SUBUNIT: Interacts with HOMER1. Interacts with AMPA receptor complexes. Interacts with SH3GL2 (endophilin-A1) (By similarity).
SUBCELLULAR LOCATION: Cell junction, synapse. Cell projection, axon. Cell projection, dendritic spine. Note=Present in both presynaptic and postsynaptic sites (By similarity).
TISSUE SPECIFICITY: Expressed in brain.
DISEASE: Defects in OPHN1 are the cause of mental retardation X- linked OPHN1-related (MRXSO) [MIM:300486]; formerly designated MRX60. MRXSO is a syndromic mental retardation. Patients present mental retardation associated with cerebellar hypoplasia and distinctive facial dysmorphism.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 1 Rho-GAP domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/OPHN1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: OPHN1
Diseases sorted by gene-association score: mental retardation, x-linked, with cerebellar hypoplasia and distinctive facial appearance* (1350), cerebellar hypoplasia (35), renpenning syndrome (9), non-syndromic x-linked intellectual disability (9), partington syndrome (8), non-syndromic intellectual disability (5), specific developmental disorder (5), autism spectrum disorder (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.94 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 126.11 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -129.60332-0.390 Picture PostScript Text
3' UTR -1470.104828-0.304 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
IPR013606 - IRSp53/MIM_homology_IMD
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR008936 - Rho_GTPase_activation_prot
IPR000198 - RhoGAP_dom

Pfam Domains:
PF00169 - PH domain
PF00620 - RhoGAP domain
PF16746 - BAR domain of APPL family

SCOP Domains:
48350 - GTPase activation domain, GAP
48371 - ARM repeat
103657 - BAR/IMD domain-like
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on O60890
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005096 GTPase activator activity
GO:0005543 phospholipid binding
GO:0035255 ionotropic glutamate receptor binding

Biological Process:
GO:0006897 endocytosis
GO:0006930 substrate-dependent cell migration, cell extension
GO:0007165 signal transduction
GO:0007399 nervous system development
GO:0007411 axon guidance
GO:0021707 cerebellar granule cell differentiation
GO:0021895 cerebral cortex neuron differentiation
GO:0030036 actin cytoskeleton organization
GO:0030100 regulation of endocytosis
GO:0030182 neuron differentiation
GO:0031175 neuron projection development
GO:0034329 cell junction assembly
GO:0035023 regulation of Rho protein signal transduction
GO:0043547 positive regulation of GTPase activity
GO:0045198 establishment of epithelial cell apical/basal polarity
GO:0048488 synaptic vesicle endocytosis
GO:0048667 cell morphogenesis involved in neuron differentiation
GO:0051056 regulation of small GTPase mediated signal transduction
GO:0051966 regulation of synaptic transmission, glutamatergic
GO:1901799 negative regulation of proteasomal protein catabolic process

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0015629 actin cytoskeleton
GO:0030054 cell junction
GO:0030424 axon
GO:0030425 dendrite
GO:0042995 cell projection
GO:0043195 terminal bouton
GO:0043197 dendritic spine
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  AJ001189 - Homo sapiens mRNA for oligophrenin 1.
BC140763 - Homo sapiens oligophrenin 1, mRNA (cDNA clone MGC:176440 IMAGE:9021631), complete cds.
AK295769 - Homo sapiens cDNA FLJ60067 complete cds, highly similar to Oligophrenin 1.
AB102656 - Homo sapiens OPHN1 mRNA for oligophrenin 1, complete cds.
AB385227 - Synthetic construct DNA, clone: pF1KB9469, Homo sapiens OPHN1 gene for oligophrenin 1, complete cds, without stop codon, in Flexi system.
BC059393 - Homo sapiens oligophrenin 1, mRNA (cDNA clone IMAGE:30344240), complete cds.
CU687370 - Synthetic construct Homo sapiens gateway clone IMAGE:100021112 5' read OPHN1 mRNA.
AK309696 - Homo sapiens cDNA, FLJ99737.
JD239812 - Sequence 220836 from Patent EP1572962.
JD554881 - Sequence 535905 from Patent EP1572962.
JD224324 - Sequence 205348 from Patent EP1572962.
JD301514 - Sequence 282538 from Patent EP1572962.
JD202999 - Sequence 184023 from Patent EP1572962.
JD492977 - Sequence 474001 from Patent EP1572962.
JD176205 - Sequence 157229 from Patent EP1572962.
JD221399 - Sequence 202423 from Patent EP1572962.
JD475479 - Sequence 456503 from Patent EP1572962.
JD297752 - Sequence 278776 from Patent EP1572962.
JD508294 - Sequence 489318 from Patent EP1572962.
JD267761 - Sequence 248785 from Patent EP1572962.
JD368889 - Sequence 349913 from Patent EP1572962.
JD215845 - Sequence 196869 from Patent EP1572962.
JD455522 - Sequence 436546 from Patent EP1572962.
JD383188 - Sequence 364212 from Patent EP1572962.
JD375416 - Sequence 356440 from Patent EP1572962.
JD184032 - Sequence 165056 from Patent EP1572962.
JD088153 - Sequence 69177 from Patent EP1572962.
JD558489 - Sequence 539513 from Patent EP1572962.
JD183444 - Sequence 164468 from Patent EP1572962.
JD115158 - Sequence 96182 from Patent EP1572962.
JD121158 - Sequence 102182 from Patent EP1572962.
JD502070 - Sequence 483094 from Patent EP1572962.
JD036747 - Sequence 17771 from Patent EP1572962.
JD455657 - Sequence 436681 from Patent EP1572962.
JD149042 - Sequence 130066 from Patent EP1572962.
JD499300 - Sequence 480324 from Patent EP1572962.
JD263596 - Sequence 244620 from Patent EP1572962.
JD459523 - Sequence 440547 from Patent EP1572962.
JD258280 - Sequence 239304 from Patent EP1572962.
JD196370 - Sequence 177394 from Patent EP1572962.
JD224831 - Sequence 205855 from Patent EP1572962.
JD235529 - Sequence 216553 from Patent EP1572962.
JD385483 - Sequence 366507 from Patent EP1572962.
JD036673 - Sequence 17697 from Patent EP1572962.
JD531216 - Sequence 512240 from Patent EP1572962.
JD236156 - Sequence 217180 from Patent EP1572962.
JD042329 - Sequence 23353 from Patent EP1572962.
JD566803 - Sequence 547827 from Patent EP1572962.
JD377872 - Sequence 358896 from Patent EP1572962.
JD099490 - Sequence 80514 from Patent EP1572962.
JD269294 - Sequence 250318 from Patent EP1572962.
JD156440 - Sequence 137464 from Patent EP1572962.
JD429234 - Sequence 410258 from Patent EP1572962.
JD565737 - Sequence 546761 from Patent EP1572962.
JD077139 - Sequence 58163 from Patent EP1572962.
JD325711 - Sequence 306735 from Patent EP1572962.
JD382351 - Sequence 363375 from Patent EP1572962.
JD488776 - Sequence 469800 from Patent EP1572962.
JD556684 - Sequence 537708 from Patent EP1572962.
AK309665 - Homo sapiens cDNA, FLJ99706.
JD470362 - Sequence 451386 from Patent EP1572962.
JD217506 - Sequence 198530 from Patent EP1572962.
JD467530 - Sequence 448554 from Patent EP1572962.
JD038136 - Sequence 19160 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_rhoPathway - Rho cell motility signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein O60890 (Reactome details) participates in the following event(s):

R-HSA-194922 GAPs inactivate Rho GTPase:GTP by hydrolysis
R-HSA-194840 Rho GTPase cycle
R-HSA-194315 Signaling by Rho GTPases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B9EIP8, ENST00000355520.1, ENST00000355520.2, ENST00000355520.3, ENST00000355520.4, ENST00000355520.5, NM_002547, O60890, OPHN1_HUMAN, Q5JQ81, Q6PCC1, Q8WX47, uc317zcv.1, uc317zcv.2
UCSC ID: ENST00000355520.6_7
RefSeq Accession: NM_002547.3
Protein: O60890 (aka OPHN1_HUMAN or OPH1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene OPHN1:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.