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    OPA3 outer mitochondrial membrane lipid metabolism regulator OPA3 [ Homo sapiens (human) ]

    Gene ID: 80207, updated on 27-Nov-2024

    Summary

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    Official Symbol
    OPA3provided by HGNC
    Official Full Name
    outer mitochondrial membrane lipid metabolism regulator OPA3provided by HGNC
    Primary source
    HGNC:HGNC:8142
    See related
    Ensembl:ENSG00000125741 MIM:606580; AllianceGenome:HGNC:8142
    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
    MGA3
    Summary
    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]
    Expression
    Ubiquitous expression in kidney (RPKM 3.0), heart (RPKM 2.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See OPA3 in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45527427..45584802, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (48354701..48412074, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46030685..46088060, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10776 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:46010402-46011186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10779 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1N (putative) Neighboring gene uncharacterized LOC107985315 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:46025801-46026353 Neighboring gene vasodilator stimulated phosphoprotein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46056279-46056909 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46056910-46057539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46061287-46061787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46065110-46065908 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46066707-46067504 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:46067505-46068302 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:46080520-46081155 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:46084233-46084733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46085233-46086168 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46086169-46087104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46100634-46101271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46101272-46101908 Neighboring gene G protein-coupled receptor 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46119367-46120205 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46120206-46121043 Neighboring gene EMAP like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46130698-46131198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10783 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46141481-46142332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46142333-46143184 Neighboring gene microRNA 330

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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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    Related articles in PubMed

    1. [On a heredo-familial disease combining cataract, optic atrophy, extrapyramidal symptoms and certain defects of Friedreich's disease. (Its nosological position in relation to the Behr's syndrome, the Marinesco-Sjogren syndrome and Friedreich's disease with ocular symptoms]. GARCIN R, et al. Rev Neurol (Paris), 1961 May. PMID 13703570
    2. 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. Anikster Y, et al. Am J Hum Genet, 2001 Dec. PMID 11668429, Free PMC Article
    3. A novel OPA3 mutation revealed by exome sequencing: an example of reverse phenotyping. Arif B, et al. JAMA Neurol, 2013 Jun. PMID 23700088
    4. A novel heterozygous OPA3 mutation located in the mitochondrial target sequence results in altered steady-state levels and fragmented mitochondrial network. Grau T, et al. J Med Genet, 2013 Dec. PMID 24136862
    5. OPA3, mutated in 3-methylglutaconic aciduria type III, encodes two transcripts targeted primarily to mitochondria. Huizing M, et al. Mol Genet Metab, 2010 Jun. PMID 20350831, Free PMC Article

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Homozygous OPA3 mutation is associated with 3-methylglutaconic aciduria type III and optic atrophy.
      Title: Novel homozygous OPA3 mutation in an Afghani family with 3-methylglutaconic aciduria type III and optic atrophy.
    2. Low OPA3 expression is associated with squamous cell carcinoma in Paranasal Sinus Neoplasms.
      Title: Putative biomarkers of malignant transformation of sinonasal inverted papilloma into squamous cell carcinoma.
    3. Mutations of the OPA3 gene can cause either autosomal dominant or autosomal recessive optic atrophy.
      Title: Mutation screening of mitochondrial DNA as well as OPA1 and OPA3 in a Chinese cohort with suspected hereditary optic atrophy.
    4. Report the results of a comprehensive study on OPA3 mutations, including the mutation spectrum and its prevalence in a large cohort of ADOA patients, the associated clinical phenotype and the functional characterisation of a newly identified OPA3 mutant.
      Title: A novel heterozygous OPA3 mutation located in the mitochondrial target sequence results in altered steady-state levels and fragmented mitochondrial network.
    5. A novel missense mutation identifies OPA3 as the cause of a complex neurological disorder with marked lower limb dystonia.
      Title: A novel OPA3 mutation revealed by exome sequencing: an example of reverse phenotyping.
    6. OPA1 mutations are the most common genetic defects identified in patients with suspected Autosomal-dominant optic atrophy (DOA), whereas OPA3 mutations are very rare in isolated optic atrophy cases.
      Title: Genetic screening for OPA1 and OPA3 mutations in patients with suspected inherited optic neuropathies.
    7. Observational study of genetic testing. (HuGE Navigator)
      Title: Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip.
    8. OPA3, as an integral mitochondrial outer membane perotein, has a crucial role in mitochondrial fission, and provides a direct link between mitochondrial morphology and optic atrophy.
      Title: Optic atrophy 3 as a protein of the mitochondrial outer membrane induces mitochondrial fragmentation.
    9. findings thus place the cellular metabolic defect of 3-methylglutaconic aciduria type III in the mitochondrion rather than the peroxisome and implicate loss of OPA3A rather than gain of OPA3B in disease etiology.
      Title: OPA3, mutated in 3-methylglutaconic aciduria type III, encodes two transcripts targeted primarily to mitochondria.
    10. The mouse ortholog of OPA3 purifies with mitochondrial inner membranes.
      Title: Proteomic analysis of the mouse liver mitochondrial inner membrane.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    3-Methylglutaconic aciduria type 3
    MedGen: C0574084 OMIM: 258501 GeneReviews: Costeff Syndrome
    		Compare labs
    Optic atrophy 3
    MedGen: C1833809 OMIM: 165300 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of comorbid depressive syndrome and alcohol dependence.
    EBI GWAS Catalog

    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

    Homology

    Clone Names

    • FLJ22187, FLJ25932, MGC75494

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in regulation of lipid metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in visual perception IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    optic atrophy 3 protein
    Names
    3-methylglutaconic aciduria type III
    OPA3 outer mitochondrial membrane lipid metabolism regulator
    Optic atrophy 3 (Iraqi-Jewish 'optic atrophy plus')
    optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)

    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_013332.1 RefSeqGene

      Range
      5063..43584
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001017989.3 → NP_001017989.2  optic atrophy 3 protein isoform a

      See identical proteins and their annotated locations for NP_001017989.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate splice site resulting in a distinct 3' coding region and 3' UTR, compared to variant 2. The resulting isoform (a) has a longer and distinct C-terminus, compared to isoform b.
      Source sequence(s)
      AC006117, BC047316, DB034102
      Consensus CDS
      CCDS33052.1
      UniProtKB/Swiss-Prot
      Q9H6K4
      Related
      ENSP00000319817.3, ENST00000323060.4
      Conserved Domains (1) summary
      pfam07047
      Location:6 → 129
      OPA3; Optic atrophy 3 protein (OPA3)

    2. NM_025136.4 → NP_079412.1  optic atrophy 3 protein isoform b

      See identical proteins and their annotated locations for NP_079412.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longer transcript but encodes the shorter isoform (b).
      Source sequence(s)
      AC006261, BC005059, BU617706, DB034102
      Consensus CDS
      CCDS12668.1
      UniProtKB/Swiss-Prot
      Q6P384, Q8N784, Q9H6K4
      Related
      ENSP00000263275.4, ENST00000263275.5
      Conserved Domains (1) summary
      pfam07047
      Location:6 → 126
      OPA3; Optic atrophy 3 protein (OPA3)

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      45527427..45584802 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006723403.5 → XP_006723466.1  optic atrophy 3 protein isoform X1

      See identical proteins and their annotated locations for XP_006723466.1

      UniProtKB/TrEMBL
      B4DK77
      Related
      ENSP00000442839.1, ENST00000544371.1
      Conserved Domains (1) summary
      pfam07047
      Location:1 → 73
      OPA3; Optic atrophy 3 protein (OPA3)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      48354701..48412074 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322228.1 → XP_054178203.1  optic atrophy 3 protein isoform X1

      UniProtKB/TrEMBL
      B4DK77
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H6K4.1 GenPept UniProtKB/Swiss-Prot:Q9H6K4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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