Submissions for variant NM_130837.3(OPA1):c.1311A>G (p.Ile437Met)

gnomAD frequency: 0.00056  dbSNP: rs143319805

Total submissions: 18

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000081747	SCV000113682	uncertain significance	not provided	2014-02-15	criteria provided, single submitter	clinical testing
GeneDx	RCV000081747	SCV000251994	pathogenic	not provided	2023-03-29	criteria provided, single submitter	clinical testing	Variant is not considered to be pathogenic when present alone, even in the homozygous state (Yu-Wai-Man et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30293569, 27290639, 31782039, 32371413, 32202296, 21636302, 24970096, 25146916, 17722006, 25012220, 28378518, 30972688, 34426522, 34242285, 32040484, 33841295, 31816670, 34732400, 28494813, 35741767, 27696015, 11440988)
Rare Disease Group, Clinical Genetics, Karolinska Institutet	RCV000677258	SCV000681433	uncertain significance	Optic nerve hypoplasia		criteria provided, single submitter	research
Mayo Clinic Laboratories, Mayo Clinic	RCV000081747	SCV000802494	uncertain significance	not provided	2023-03-20	criteria provided, single submitter	clinical testing	PP3
Invitae	RCV000081747	SCV001035176	pathogenic	not provided	2024-01-29	criteria provided, single submitter	clinical testing	This sequence change replaces isoleucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 382 of the OPA1 protein (p.Ile382Met). This variant is present in population databases (rs143319805, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with Behr syndrome and/or optic atrophy plus, Behr syndrome, optic neuropathy (PMID: 21636302, 24970096, 25012220, 25146916, 28494813, 30972688, 33841295, 35741767). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. The effect of this variant on homozygous individuals has not been well documented in the literature (PMID: 24970096). Heterozygous individuals may either have mild disease symptoms or be unaffected (PMID:18496845, 19319978, 25012220, 27290639, 32040484). It has also been observed to segregate with disease in related individuals. This variant is also known as c.1311A>G/p.I437M. ClinVar contains an entry for this variant (Variation ID: 50866). 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 with a positive predictive value of 80%. Studies have shown that this missense change alters OPA1 gene expression (PMID: 24970096, 30293569). For these reasons, this variant has been classified as Pathogenic.
Mendelics	RCV000043607	SCV001136663	uncertain significance	Autosomal dominant optic atrophy classic form	2019-05-28	criteria provided, single submitter	clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV000210748	SCV001366678	likely pathogenic	Abortive cerebellar ataxia	2019-06-10	criteria provided, single submitter	clinical testing	This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS3,PM3,PP3,PP5.
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital	RCV001249638	SCV001423605	uncertain significance	Abortive cerebellar ataxia; Optic atrophy with or without deafness, ophthalmoplegia, myopathy, ataxia, and neuropathy; Autosomal dominant optic atrophy classic form	2017-09-20	criteria provided, single submitter	clinical testing	[ACMG/AMP: PM1, PM3, PP1, PP3; BS3] This alteration is located in a mutational hotspot and/or critical and well-established functional domain [PM1], is detected in trans with a known pathogenic variant [PM3], has been shown to cosegregate with disease in multiple affected family members [PP1].
Ambry Genetics	RCV001267306	SCV001445487	pathogenic	Inborn genetic diseases	2020-03-16	criteria provided, single submitter	clinical testing	The c.1146A>G (p.I382M) alteration is located in exon 12 (coding exon 12) of the OPA1 gene. This alteration results from an A to G substitution at nucleotide position 1146, causing the isoleucine (I) at amino acid position 382 to be replaced by a methionine (M). Based on the available evidence, the OPA1 c.1146A>G (p.I382M) alteration is classified as pathogenic for autosomal recessive Behr syndrome; however, it is unlikely to be causative of autosomal dominant OPA1-related optic atrophy or autosomal dominant OPA1-related optic atrophy plus syndrome. Based on data from gnomAD, the G allele has an overall frequency of 0.06% (166/282274) total alleles studied. The highest observed frequency was 0.1% (30/30614) of South Asian alleles. This alteration has been described in trans with a pathogenic alteration in multiple families presenting with early-onset optic atrophy and variable additional abnormalities which can include neuropathy, ataxia, spasticity, hypotonia, dysphagia, gastrointestinal dysmotility, and neurodevelopmental delay. The c.1146A>G (p.I382M) alteration alone is not observed to be disease-causing in either the homozygous or heterozygous state, but has clinical implications when occurring in trans with another pathogenic allele (Bonifert, 2014; Nasca, 2017; Schaaf, 2011). This alteration is also reported as p.I437M in the literature. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
Baylor Genetics	RCV000043607	SCV001524291	uncertain significance	Autosomal dominant optic atrophy classic form	2020-03-21	criteria provided, single submitter	clinical testing	This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Athena Diagnostics	RCV000081747	SCV002771114	uncertain significance	not provided	2022-08-25	criteria provided, single submitter	clinical testing
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV000210748	SCV003807267	pathogenic	Abortive cerebellar ataxia	2023-04-05	criteria provided, single submitter	clinical testing	ACMG classification criteria: PM3 very strong, PP1 supporting, PP3 supporting
Neuberg Centre For Genomic Medicine, NCGM	RCV000210748	SCV004048348	pathogenic	Abortive cerebellar ataxia		criteria provided, single submitter	clinical testing	The c.1311A>G p.Ile437Met variant in OPA1 gene has been reported in heterozygous as well as compound heterozygous state in individuals (Schaaf CP et al). Experimental studies have shown a damaging effect (Alessia Nasca et al,2017). This variant is reported with the allele frequency 0.05% in the gnomad and novel in 1000 genome database. It has been submitted to ClinVar with varying interpretations: Likely Pathogenic/Pathogenic/Uncertain Significance/Likely Benign. The amino acid Ile at position 437 is changed to a Met changing protein sequence and it might alter its composition and physico-chemical properties The variant is predicted to be damaging by both SIFT and PolyPhen2. The residue is conserved across species. The amino acid change p.Ile437Met in OPA1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.
PreventionGenetics, part of Exact Sciences	RCV004537182	SCV004740804	uncertain significance	OPA1-related disorder	2023-12-12	criteria provided, single submitter	clinical testing	The OPA1 c.1311A>G variant is predicted to result in the amino acid substitution p.Ile437Met. This variant (also known as c.1146A>G [p.Ile382Met] in transcript NM_015560.2) has been reported in the heterozygous state in patients with autosomal dominant optic atrophy (Schimpf et al. 2008. PubMed ID: 17722006; Ferré et al. 2009. PubMed ID: 19319978; Carelli et al. 2015. PubMed ID: 25146916). However, other individuals who carried this variant in the heterozygous or even homozygous states were reportedly asymptomatic (Bonifert et al. 2014. PubMed ID: 24970096; Bonneau et al. 2014. PubMed ID: 25012220; Carelli et al. 2015. PubMed ID: 25146916). Several reports indicate that this variant may possibly be a mild pathogenic variant that contributes to increased severity of disease when present in the compound heterozygous state with a known pathogenic variant (Bonifert et al. 2014. PubMed ID: 24970096; Bonneau et al. 2014. PubMed ID: 25012220; Nasca et al. 2017. PubMed ID: 28494813). This variant has been classified as likely benign, uncertain, likely pathogenic, and pathogenic in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/50866). This variant is reported in 0.098% of alleles in individuals of South Asian descent in gnomAD, including >150 heterozygotes in the entire gnomAD population database. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV003993775	SCV004813105	uncertain significance	not specified	2024-02-06	criteria provided, single submitter	clinical testing	Variant summary: OPA1 c.1146A>G (p.Ile382Met) results in a conservative amino acid change located in the Dynamin GTPase domain (IPR001401) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00087 in 1607894 control chromosomes in the gnomAD database, including 3 homozygotes. c.1146A>G (also known as c.1311A>G/p.I437M) has been reported in the literature in multiple compound heterozygous individuals affected with Behr syndrome and/or optic atrophy (examples: Schaaf_2011, Bonifert_2014, Bonneau_2014, Nasca_2017, Carelli_2015, Zerem_2019, Othman_2022). In these studies, c.1146A>G variant was inherited from an asymptomatic parent, and at-least one parent was homozygous for this variant (Bonifert_ 2014). It has also been reported in heterozygous state in individuals affected with mitochondrial disorder (Pronicka_2016) and inherited optic neuropathy (Charif_ 2021) without strong evidence for causality. At least one publication reports experimental evidence using a yeast complementation assay that this variant has a very mild growth defect only at dilute concentrations (example: Nasca_2017). Taken together, these results suggest c.1146A>G pathogenic effect is dependent on the presence of a second pathogenic allele in trans. ClinVar contains an entry for this variant (Variation ID: 50866). The following publications have been ascertained in the context of this evaluation (PMID: 28494813, 24970096, 21636302, 25012220 , 25146916, 33841295, 30972688, 27290639, 31816670, 35741767). Based on the evidence outlined above, the variant was classified as uncertain significance for Autosomal Dominant OPA1-Related Disorders.
Baylor Genetics	RCV004537182	SCV005049782	likely pathogenic	OPA1-related disorder	2024-01-17	criteria provided, single submitter	clinical testing
OMIM	RCV000043607	SCV000071625	pathogenic	Autosomal dominant optic atrophy classic form	2011-08-01	no assertion criteria provided	literature only
OMIM	RCV000210748	SCV000266835	pathogenic	Abortive cerebellar ataxia	2011-08-01	no assertion criteria provided	literature only