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

Gene ID: 80207, updated on 5-Mar-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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Location:
19q13.32
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45527427..45584802, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (48354701..48412074, complement)
105.20220307 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. Novel homozygous OPA3 mutation in an Afghani family with 3-methylglutaconic aciduria type III and optic atrophy. Gaier ED, et al. Ophthalmic Genet, 2019 Dec. PMID 31928268, Free PMC Article
  2. 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
  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. 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
  5. Costeff Syndrome. Adam MP, et al. , 1993. PMID 20301646

See all (44) 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)

Genotypes

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 response to stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
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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NEW Try the new Transcript table

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_2023_10

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

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