ClinVar Genomic variation as it relates to human health
NM_130837.3(OPA1):c.1499G>A (p.Arg500His)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_130837.3(OPA1):c.1499G>A (p.Arg500His)
Variation ID: 5091 Accession: VCV000005091.30
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3q29 3: 193643996 (GRCh38) [ NCBI UCSC ] 3: 193361785 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Oct 20, 2024 Mar 14, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_130837.3:c.1499G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_570850.2:p.Arg500His missense NM_001354663.2:c.965G>A NP_001341592.1:p.Arg322His missense NM_001354664.2:c.962G>A NP_001341593.1:p.Arg321His missense NM_015560.3:c.1334G>A NP_056375.2:p.Arg445His missense NM_130831.3:c.1226G>A NP_570844.1:p.Arg409His missense NM_130832.3:c.1280G>A NP_570845.1:p.Arg427His missense NM_130833.3:c.1337G>A NP_570846.1:p.Arg446His missense NM_130834.3:c.1388G>A NP_570847.2:p.Arg463His missense NM_130835.3:c.1391G>A NP_570848.1:p.Arg464His missense NM_130836.3:c.1445G>A NP_570849.2:p.Arg482His missense NC_000003.12:g.193643996G>A NC_000003.11:g.193361785G>A NG_011605.1:g.55853G>A LRG_337:g.55853G>A LRG_337t1:c.1334G>A LRG_337p1:p.Arg445His O60313:p.Arg445His - Protein change
- R500H, R409H, R322H, R463H, R427H, R321H, R446H, R464H, R482H
- Other names
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R445H
- Canonical SPDI
- NC_000003.12:193643995:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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OPA1 | - | - |
GRCh38 GRCh37 |
1285 | 1477 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (2) |
no assertion criteria provided
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Nov 25, 2008 | RCV000005396.13 | |
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Apr 16, 2023 | RCV000081749.36 | |
Pathogenic (1) |
no assertion criteria provided
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Apr 7, 2017 | RCV000508953.9 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 14, 2024 | RCV003137493.11 | |
OPA1-related disorder
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Pathogenic (1) |
criteria provided, single submitter
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Dec 1, 2023 | RCV003492285.1 |
Likely pathogenic (1) |
criteria provided, single submitter
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Mar 1, 2024 | RCV004585987.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Jan 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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Autosomal dominant optic atrophy classic form
Affected status: yes
Allele origin:
germline
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Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
Accession: SCV003807194.1
First in ClinVar: Mar 04, 2023 Last updated: Mar 04, 2023 |
Comment:
ACMG classification criteria: PS3 supporting, PS4 strong, PM2 moderated, PM6 moderated, PP1 supporting, PP3 supporting
Number of individuals with the variant: 1
Clinical Features:
Visual impairment (present) , Morphological central nervous system abnormality (present) , Progressive visual loss (present) , Sensorineural hearing loss disorder (present) , Postlingual sensorineural hearing … (more)
Visual impairment (present) , Morphological central nervous system abnormality (present) , Progressive visual loss (present) , Sensorineural hearing loss disorder (present) , Postlingual sensorineural hearing impairment (present) , Childhood onset sensorineural hearing impairment (present) , Visual loss (present) , Optic atrophy (present) (less)
Geographic origin: Brazil
Method: Paired-end whole-genome sequencing
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Pathogenic
(Mar 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV003916870.13
First in ClinVar: Apr 23, 2023 Last updated: Oct 20, 2024 |
Comment:
OPA1: PS2, PM2, PP1, PP3, PP4, PS3:Supporting
Number of individuals with the variant: 1
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Pathogenic
(May 29, 2013)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000226147.5
First in ClinVar: Jun 28, 2015 Last updated: Jul 31, 2019 |
Number of individuals with the variant: 4
Zygosity: Single Heterozygote
Sex: mixed
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Pathogenic
(Jun 17, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001762022.1
First in ClinVar: Jul 31, 2021 Last updated: Jul 31, 2021 |
Clinical Features:
Optic atrophy (present)
Sex: female
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Pathogenic
(Dec 15, 2020)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000252017.14
First in ClinVar: Oct 11, 2015 Last updated: Feb 15, 2018 |
Comment:
Published functional studies demonstrate a damaging effect (Del Dotto et al., 2018; Ban et al., 2010); Not observed in large population cohorts (Lek et al., … (more)
Published functional studies demonstrate a damaging effect (Del Dotto et al., 2018; Ban et al., 2010); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 25564500, 28841713, 20157015, 27696015, 32202296, 22800932, 16240368, 20185555, 14644237, 25641387, 18158317, 20952381, 28941528, 30293569, 31673222, 28494813, 29952689, 28378518, 28926202, 31609081, 19733158, 20385391, 12566046, 32025183, 33231680, 31500643) (less)
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Pathogenic
(Dec 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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OPA1-Related Disorders
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004240805.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
Comment:
Variant summary: OPA1 c.1334G>A (p.Arg445His) results in a non-conservative amino acid change located in the Dynamin, GTPase domain (IPR001401) of the encoded protein sequence. Five … (more)
Variant summary: OPA1 c.1334G>A (p.Arg445His) results in a non-conservative amino acid change located in the Dynamin, GTPase domain (IPR001401) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251254 control chromosomes (gnomAD). c.1334G>A has been reported in the literature in multiple individuals affected with dominant optic atrophy and this variant co-segregated with disease (Payne_2004, Leruez_2013). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and this variant reduced levels of GTP hydrolysis (Ban_2010). The following publications have been ascertained in the context of this evaluation (PMID: 20185555, 24798923, 15531309). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Apr 16, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001591732.3
First in ClinVar: May 10, 2021 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, … (more)
For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt OPA1 protein function. ClinVar contains an entry for this variant (Variation ID: 5091). This missense change has been observed in individual(s) with dominant optic atrophy (PMID: 18158317, 28926202, 31673222). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 445 of the OPA1 protein (p.Arg445His). (less)
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Pathogenic
(Mar 14, 2024)
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criteria provided, single submitter
Method: research
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Autosomal dominant optic atrophy classic form
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004801269.2
First in ClinVar: Mar 16, 2024 Last updated: Apr 06, 2024 |
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Likely pathogenic
(Mar 01, 2024)
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criteria provided, single submitter
Method: research
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Centronuclear myopathy
Affected status: yes
Allele origin:
biparental
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Muscle and Diseases Team, Institut de Génétique et Biologie Moléculaire et Cellulaire
Accession: SCV005038606.1
First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024 |
Comment:
PM1+PM2+PM5+PP3+PP5
Number of individuals with the variant: 1
Sex: male
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Pathogenic
(Apr 07, 2017)
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no assertion criteria provided
Method: clinical testing
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Mitochondrial disease
Affected status: yes
Allele origin:
germline
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Wellcome Centre for Mitochondrial Research, Newcastle University
Accession: SCV000575920.1
First in ClinVar: May 22, 2017 Last updated: May 22, 2017 |
Number of individuals with the variant: 1
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Pathogenic
(Nov 25, 2008)
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no assertion criteria provided
Method: literature only
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OPTIC ATROPHY WITH OR WITHOUT DEAFNESS, OPHTHALMOPLEGIA, MYOPATHY, ATAXIA, AND NEUROPATHY
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000025576.2
First in ClinVar: Apr 04, 2013 Last updated: Oct 25, 2021 |
Comment on evidence:
In a Japanese patient with optic atrophy and moderate sensorineural deafness (125250), Shimizu et al. (2003) identified a heterozygous G-to-A transition in the second nucleotide … (more)
In a Japanese patient with optic atrophy and moderate sensorineural deafness (125250), Shimizu et al. (2003) identified a heterozygous G-to-A transition in the second nucleotide at codon 445 in the OPA1 gene, resulting in an arg445-to-his (R445H) substitution in the GTPase domain. Payne et al. (2004) found this mutation in a large Utah family and an unrelated Belgian family, previously described by Treft et al. (1984) and Meire et al. (1985), respectively. Both families had optic atrophy, deafness, and ophthalmoplegia. The authors hypothesized that, although OPA1 is a nuclear gene, the localization of its gene product to mitochondria suggests that mitochondrial dysfunction might be the final common pathway for many forms of syndromic and nonsyndromic optic atrophy, hearing loss, and external ophthalmoplegia. In a third family with optic atrophy and hearing loss, unrelated to the Utah or Belgian families, Li et al. (2005) identified the R445H mutation. Li et al. (2005) noted that affected members of this family did not have extraocular motility abnormalities or ptosis, thus illustrating the intra- and interfamilial phenotype variability associated with this mutation. Amati-Bonneau et al. (2005) identified the R445H mutation in 5 unrelated patients from 4 families with optic atrophy and deafness, thus confirming that this mutation is specifically associated with hearing loss. One of the patients had been previously reported by Amati-Bonneau et al. (2003). In the Spanish mother and daughter previously reported by Amati-Bonneau et al. (2005), Amati-Bonneau et al. (2008) noted that the mother had additional features including myopathy, neuropathy, and progressive external ophthalmoplegia. Stewart et al. (2008) identified the R445H mutation in 2 probands with optic atrophy and myopathy associated with mitochondrial DNA deletions. One proband also had deafness. The other proband did not have hearing loss, but 3 affected family members had hearing loss. In a 27-year-old Italian woman and her 57-year-old mother with DOA+, Napolitano et al. (2020) identified heterozygosity for the mutation in the OPA1 gene (R445H; 605290.0011). The mutation was identified by Sanger sequencing of the OPA1 gene. The daughter had reduced visual acuity, deafness, and myopathy, and her mother had amaurosis, deafness, extraocular muscle palsy, and severe ataxia. Expression of HTRA2 (606441) was increased in the muscle tissue of both patients, although more so in the daughter. Napolitano et al. (2020) hypothesized that OPA1 mutations may induce HTRA2 overexpression, and variable expression of HTRA2 may contribute to disease variability in optic atrophy and deafness in patients with the same OPA1 mutation. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Optic atrophy with or without deafness, ophthalmoplegia, myopathy, ataxia, and neuropathy
Affected status: not provided
Allele origin:
unknown
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GeneReviews
Accession: SCV000041283.2
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Exome sequencing in undiagnosed congenital myopathy reveals new genes and refines genes-phenotypes correlations. | de Feraudy Y | Genome medicine | 2024 | DOI: 10.1186/s13073-024-01353-0 |
Intrafamilial "DOA-plus" phenotype variability related to different OMI/HTRA2 expression. | Napolitano F | American journal of medical genetics. Part A | 2020 | PMID: 31609081 |
Autosomal dominant optic atrophy with OPA1 gene mutations accompanied by auditory neuropathy and other systemic complications in a Japanese cohort. | Maeda-Katahira A | Molecular vision | 2019 | PMID: 31673222 |
Retinal dysfunction characterizes subtypes of dominant optic atrophy. | Cascavilla ML | Acta ophthalmologica | 2018 | PMID: 28926202 |
Decreased male reproductive success in association with mitochondrial dysfunction. | Martikainen MH | European journal of human genetics : EJHG | 2017 | PMID: 28812649 |
Optic Atrophy Type 1 – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY. | Adam MP | - | 2015 | PMID: 20301426 |
Mitochondrial dysfunction affecting visual pathways. | Leruez S | Revue neurologique | 2014 | PMID: 24798923 |
OPA1 disease alleles causing dominant optic atrophy have defects in cardiolipin-stimulated GTP hydrolysis and membrane tubulation. | Ban T | Human molecular genetics | 2010 | PMID: 20185555 |
OPA1 in multiple mitochondrial DNA deletion disorders. | Stewart JD | Neurology | 2008 | PMID: 19029523 |
OPA1 mutations induce mitochondrial DNA instability and optic atrophy 'plus' phenotypes. | Amati-Bonneau P | Brain : a journal of neurology | 2008 | PMID: 18158317 |
OPA1 R445H mutation in optic atrophy associated with sensorineural deafness. | Amati-Bonneau P | Annals of neurology | 2005 | PMID: 16240368 |
Optic atrophy and sensorineural hearing loss in a family caused by an R445H OPA1 mutation. | Li C | American journal of medical genetics. Part A | 2005 | PMID: 16158427 |
Dominant optic atrophy, sensorineural hearing loss, ptosis, and ophthalmoplegia: a syndrome caused by a missense mutation in OPA1. | Payne M | American journal of ophthalmology | 2004 | PMID: 15531309 |
The association of autosomal dominant optic atrophy and moderate deafness may be due to the R445H mutation in the OPA1 gene. | Amati-Bonneau P | American journal of ophthalmology | 2003 | PMID: 14644237 |
A novel mutation in the OPA1 gene in a Japanese patient with optic atrophy. | Shimizu S | American journal of ophthalmology | 2003 | PMID: 12566046 |
Dominant optic nerve atrophy with progressive hearing loss and chronic progressive external ophthalmoplegia (CPEO). | Meire F | Ophthalmic paediatrics and genetics | 1985 | PMID: 4058877 |
Dominant optic atrophy, deafness, ptosis, ophthalmoplegia, dystaxia, and myopathy. A new syndrome. | Treft RL | Ophthalmology | 1984 | PMID: 6493699 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=OPA1 | - | - | - | - |
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Text-mined citations for rs80356529 ...
HelpRecord last updated Dec 07, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.