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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

OPA3 Gene

protein-coding   GIFtS: 47
GCID: GC19M046031

optic atrophy 3 (autosomal recessive, with chorea and spastic...

 Explore 21 diseases affiliated with
OPA3 via our new
 Human Malady Compendium 
Biological research products
for OPA3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Optic Atrophy 3 (Autosomal Recessive, With Chorea And Spastic
Paraplegia)1 2
MGA31 2 5
FLJ221871
Optic Atrophy 3 (Iraqi-Jewish 'Optic Atrophy Plus')2
Optic Atrophy 3 Protein2

External Ids:    HGNC: 81421   Entrez Gene: 802072   Ensembl: ENSG000001257417   OMIM: 6065805   UniProtKB: Q9H6K43   

Export aliases for OPA3 gene to outside databases

Previous GC identifers: GC19M046699 GC19M046421 GC19M050706 GC19M050722 GC19M050747 GC19M042461


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for OPA3:
The mouse ortholog of this protein co-purifies with the mitochondrial inner membrane. Mutations in this gene have been
shown to result in 3-methylglutaconic aciduria type III and autosomal dominant optic atrophy and cataract. Multiple
transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Oct 2009)

UniProtKB/Swiss-Prot: OPA3_HUMAN, Q9H6K4
Function: May play some role in mitochondrial processes

Gene Wiki entry for OPA3


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.1  NT_011109.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the OPA3 gene promoter:
         AP-2rep   NF-1   AML1a   Sp1   GATA-1   Arnt   GATA-2   ZIC2/Zic2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidOPA3 promoter sequence
   Search SABiosciences Chromatin IP Primers for OPA3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat OPA3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.32   Ensembl cytogenetic band:  19q13.32   HGNC cytogenetic band: 19q13.2-q13.3

OPA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
OPA3 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M046031:  view genomic region     (about GC identifiers)

Start:
46,030,685 bp from pter      End:
46,105,470 bp from pter
Size:
74,786 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: OPA3_HUMAN, Q9H6K4 (See protein sequence)
Recommended Name: Optic atrophy 3 protein  
Size: 179 amino acids; 19996 Da
Subcellular location: Mitochondrion (Probable)
Secondary accessions: Q6P384 Q8N784
Alternative splicing: 2 isoforms:  Q9H6K4-1   Q9H6K4-2   (Ref.2 (BAC05415) sequence is in conflict in position: 130:G->E)

Explore the universe of human proteins at neXtProt for OPA3: NX_Q9H6K4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H6K4

  • OPA3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001017989.2  NP_079412.1  

    ENSEMBL proteins: 
     ENSP00000319817   ENSP00000263275   ENSP00000442839  

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    Uscn Proteins for OPA3

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion NAS11668429


    OPA3 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    OPA3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR010754 OPA3-like

    Graphical View of Domain Structure for InterPro Entry Q9H6K4

    ProtoNet protein and cluster: Q9H6K4

    1 Blocks protein family: IPB010754 Optic atrophy 3

    UniProtKB/Swiss-Prot: OPA3_HUMAN, Q9H6K4
    Similarity: Belongs to the OPA3 family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: OPA3_HUMAN, Q9H6K4
    Function: May play some role in mitochondrial processes

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    1 GenomeRNAi human phenotype for OPA3:
     Decreased number of cells in m 

    Animal Models:
         13 MGI mutant phenotypes (inferred from 1 allele(MGI details for Opa3):
     adipose tissue  behavior/neurological  cardiovascular system  cellular  craniofacial 
     growth/size  homeostasis/metabolism  liver/biliary system  mortality/aging  muscle 
     nervous system  skeleton  vision/eye 

    OPA3 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for OPA3

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007601visual perception IMP15342707
    GO:0050896response to stimulus IEA--


    OPA3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    OPA3 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for OPA3
    1 Novoseek chemical compound relationship for OPA3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    3-methylglutaconic acid 96.4 1 20350831 (1)

    Search CenterWatch for drugs/clinical trials and news about OPA3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for OPA3 gene (2 alternative transcripts): 
    NM_001017989.2  NM_025136.3  

    Unigene Cluster for OPA3:

    Optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)
    Hs.466945  [show with all ESTs]
    Unigene Representative Sequence: NM_025136
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000323060(uc002pcj.4) ENST00000263275(uc002pck.4 uc010xxk.2)
    ENST00000544371

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    hsa-miR-1321 hsa-miR-185* hsa-let-7d hsa-miR-1260b hsa-let-7c hsa-let-7g hsa-let-7a hsa-miR-98
    SwitchGear 3'UTR luciferase reporter plasmidOPA3 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK025840.1 AK098798.1 AK296429.1 BC005059.1 BC047316.1 BC064146.1 

    13 DOTS entries:

    DT.40198663  DT.100677851  DT.100754455  DT.95228567  DT.100700817  DT.100686228  DT.40250356  DT.91736985 
    DT.100737665  DT.100733332  DT.100766382  DT.121499779  DT.406032 

    24/74 AceView cDNA sequences (see all 74):

    BC064146 BU501496 BQ013305 AI087335 BC047316 BU164977 CA306826 BM727436 
    BM464645 BI768149 BM126314 BP341595 AI143727 BE336754 BG832005 BE206133 
    CD110193 CK818906 BG396192 AI275146 BC005059 BX498648 BU740898 NM_025136 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    OPA3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See OPA3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for OPA3

    SOURCE GeneReport for Unigene cluster: Hs.466945

    UniProtKB/Swiss-Prot: OPA3_HUMAN, Q9H6K4
    Tissue specificity: Ubiquitous. Most prominent expression in skeletal muscle and kidney

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OPA3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for OPA3 gene from 7/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Opa31 , 5 optic atrophy 3 (human)5
    optic atrophy 31
    80.08(n)1
    76.83(a)1
      7 (9.48 cM)5
    4031871  NM_207525.31  NP_997408.21 
     192283345 
    lizard
    (Anolis carolinensis)
    Reptilia OPA36
    --
    59(a)
    1 ↔ 1
    GL344188.1(45741-49849)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.44512 Transcribed sequence with weak similarity to protein more 71.58(n)    AL891596.2 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.248962 Danio rerio, Similar to optic atrophy 3 (autosomal more 73.99(n)    BC049503.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG136011 CG13601 55.18(n)
    43.24(a)
      42826  NM_142935.2  NP_651192.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G285106
    AT3G581506
    Optic atrophy 3 protein (OPA3)
    24(a)
    22(a)
    many → 1
    many → 1
    1(10023876-10026295)
    3(21532813-21534089)
    rice
    (Oryza sativa)
    Liliopsida --
    --
    (see all 3)
    expressed protein
    (see all 3)
    30(a)
    29(a)
    (see all 3)
    many → 1
    many → 1
    (see all 3)
    1(7851645-7854833)
    2(12320247-12324027)


    ENSEMBL Gene Tree for OPA3 (if available)
    TreeFam Gene Tree for OPA3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1079 NCBI SNPs in OPA3 are shown (see all 1079    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs38268601,2
    C,F,A,H,non-pathogenic46057081(-) GCAGCC/TGAGCT 3 A int1 syn1 ese315Minor allele frequency- T:0.32NA WA CSA EA EU 4495
    rs803565251,2
    Cpathogenic46056999(-) GCCACC/GAGGCG 3 Q E int1 mis10--------
    rs803565241,2
    Cpathogenic46057035(-) TCGTGA/GGCGGC 3 S G mis1 int10--------
    rs1484349991,2
    --46030848(+) TTTTCA/GTAGAG 1 -- int10--------
    rs612675721,2
    C,F,--46030879(+) CTAGGT/CTGGTC 1 -- int15Minor allele frequency- C:0.25WA CSA NA EA 362
    rs1160463571,2
    F,--46030951(+) CGTGAG/TCCACT 1 -- int11Minor allele frequency- T:0.13WA 118
    rs1163294071,2
    C,F,--46030952(+) GTGAGC/TCACTG 1 -- int11Minor allele frequency- T:0.13WA 118
    rs22701991,2
    C,H,--46031065(+) AACGCT/GGACAG 1 -- ut31 ese34Minor allele frequency- G:0.00NS EA 418
    rs1425456641,2
    --46031074(+) AGTCGA/GTTTAT 1 -- ut310--------
    rs1509860931,2
    --46031177(+) AGGGGG/TACCTC 1 -- ut310--------

    HapMap Linkage Disequilibrium report for OPA3 (46030685 - 46105470 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for OPA3: --
    Human Gene Mutation Database (HGMD): OPA3

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    OPA3 for disorders           About GeneDecksing

    OMIM gene information: 606580   
    OMIM disorders: 258501  165300  
    UniProtKB/Swiss-Prot: OPA3_HUMAN, Q9H6K4
  • Defects in OPA3 are the cause of 3-methylglutaconic aciduria type 3 (MGA3) [MIM:258501]; also known as optic
  • atrophy plus syndrome or Costeff optic atrophy syndrome. MGA3 is an autosomal recessive neuro-ophthalmologic syndrome
    consisting of early-onset bilateral optic atrophy, spasticity, extrapyramidal dysfunction, and cognitive deficit.
    Urinary excretion of 3-methylglutaconic acid and 3-methylglutaric acid is increased. MGA3 can be distinguished from
    MGA1 by the absence of increase of 3-hydroxyisovaleric acid levels
  • Defects in OPA3 are the cause of optic atrophy type 3 (OPA3) [MIM:165300]; also known as autosomal dominant
  • optic atrophy and cataract (ADOAC) or cataract, optic atrophy and neurologic disorder. Hereditary optic atrophy form a
    heterogeneous group of disorders. The autosomal dominant forms are characterized by an insidious onset of visual
    impairment in early childhood with moderate to severe loss of visual acuity, temporal optic disk pallor, color vision
    deficits and centrocecal scotoma of variable density

    20/21 diseases for OPA3 (see all 21):    About MalaCards
    optic atrophy    3-methylglutaconic aciduria    optic atrophy and cataract    spastic paraplegia
    3-methylglutaconic aciduria type 3    chorea    cataract    marinesco-sjogren syndrome
    paraplegia    leigh-like syndrome    leber hereditary optic neuropathy    spasticity
    behr syndrome    scotoma    myotonic dystrophy    sjogren's syndrome
    wolfram syndrome    neuropathy    retinal disease    retinitis

    2 diseases from the University of Copenhagen DISEASES database for OPA3:
    Optic atrophy     Leber hereditary optic neuropathy

    2 Novoseek disease relationships for OPA3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    optic atrophy 87.2 7 11668429 (2), 15902555 (1), 15924081 (1), 20350831 (1) (see all 5)
    developmental delay 55.8 1 15902555 (1)

    GeneTests: OPA3
    3-Methylglutaconic Aciduria Type 3

    Human Genome Epidemiology (HuGE) Navigator: OPA3 (4 documents)

    Export disorders for OPA3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for OPA3 gene, integrated from 9 sources (see all 31):
    (articles sorted by number of sources associating them with OPA3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Type III 3-methylglutaconic aciduria (optic atrophy plus syndrome, or Costeff optic atrophy syndrome): identification of the OPA3 gene and its founder mutation in Iraqi Jews. (PubMed id 11668429)1, 2, 3, 9 Anikster Y.... Elpeleg O. (2001)
    2. OPA3 gene mutations responsible for autosomal dominant optic atrophy and cataract. (PubMed id 15342707)1, 2 Reynier P....Bonneau D. (2004)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. Iraqi-Jewish kindreds with optic atrophy plus (3-methylglutaconic aciduria type 3) demonstrate linkage disequilibrium with the CTG repeat in the 3' untranslated region of the myotonic dystrophy protein kinase gene. (PubMed id 9097959)1, 3 Nystuen A....Sheffield V.C. (1997)
    6. OPA3, mutated in 3-methylglutaconic aciduria type III , encodes two transcripts targeted primarily to mitochondria. (PubMed id 20350831)1, 9 Huizing M....Anikster Y. (2010)
    7. [Costeff syndrome: a syndrome that was described in Israel and the responsible gene discovered by an Israeli doctor] (PubMed id 16838891)1, 9 Fink N. and Mouallem M. (2006)
    8. Genome-wide association study of comorbid depressive s yndrome and alcohol dependence. (PubMed id 22064162)1 Edwards A.C....Dick D.M. (2012)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    10. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 80207 HGNC: 8142 AceView: OPA3 Ensembl:ENSG00000125741 euGenes: HUgn80207
    ECgene: OPA3 H-InvDB: OPA3

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for OPA3 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/OPA3

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