ClinVar Genomic variation as it relates to human health

This NDUFV1 variant (rs536758576) is rare (<0.1%) in a large population dataset (gnomAD: 14/282690 total alleles; 0.005%; no homozygotes) and has been reported in ClinVar. It has been reported in a homozygous and compound heterozygous state in individuals with mitochondrial complex I deficiency. A different pathogenic variant, p.Arg386Cys, has also been reported at this amino acid position8. Three bioinformatic tools queried predict that the p.(Arg386His) substitution would be damaging, and the arginine residue at this position is strongly conserved across the vertebrate species assessed. This substitution is predicted to disrupt the protein–protein interactions that facilitate Fe–S cluster buffering and showed evidence of impaired complex I activity in a yeast model system. Bioinformatic analysis predicts that this variant would not affect normal exon 8 splicing, although this has not been confirmed experimentally to our knowledge. This variant alone is not expected to cause disease. We consider this variant to be likely pathogenic.

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.005%). Missense changes are a common disease-causing mechanism. The variant was found to in trans with other pathogenic variant (3billion dataset). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.96; 3Cnet: 0.67). Same nucleotide change resulting in same amino acid change (ClinVar ID: VCV000496918 ) and different missense changes at the same codon (p.Arg386Cys, p.Arg386Leu; ClinVar ID: VCV000419230 , VCV001465562 ) have been previously reported as pathogenic/likely pathogenic with strong evidence. Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

Variant summary: NDUFV1 c.1157G>A (p.Arg386His) results in a non-conservative amino acid change located in the iron-sulphur binding domain (IPR019575) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.6e-05 in 251346 control chromosomes (gnomAD). c.1157G>A has been reported in the literature as a biallelic genotype in multiple individuals affected with Leigh Syndrome/complex I deficiency who have been comprehensively genotyped (sequencing/homozygosity mapping approaches) (e.g. Calvo_2010, Swalwell_2011, Vilain_2012, French_2022, Tang_2022). These data indicate that the variant is very likely to be associated with disease. An experimental study evaluating the impact of the variant on protein function in a yeast model system reported decreased flavin content, intermediate complex 1 activity, and slight destablilization; however, these findings do not necessarily allow for convincing conclusions about the variant effect in vivo due to the nature of the experimental system employed (Varghese_2015). Another variant affecting the same amino acid (c.1156C>T, p.Arg386Cys) has also been observed in affected individuals and is classified as pathogenic/likely pathogenic in ClinVar, suggesting that R386 may be important for protein function. The following publications have been ascertained in the context of this evaluation (PMID: 25615419, 20818383, 23562761, 29976978, 21364701, 26345448, 21696386, 35586607, 35482246). Seven submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as either pathogenic (n=5)/likely pathogenic (n=1) or VUS (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.

The NDUFV1 c.1157G>A variant is predicted to result in the amino acid substitution p.Arg386His. This variant, along with a second potentially causative variant in NDUFV1, has been reported in two patients with mitochondrial complex I deficiency (Calvo et al. 2010. PubMed ID: 20818383, see supplementary table 2). This variant in the homozygous state has been reported in two consanguineous siblings with brainstem lesions and Leigh syndrome; both of their unaffected parents are heterozygous for this variant (Vilain et al. 2012. PubMed ID: 21696386, reported as c.1156G>A, p.Arg386His). A different variant affecting the same amino acid (p.Arg386Cys) has also been reported to be pathogenic (Srivastava et al. 2018. PubMed ID: 29976978; Breningstall et al. 2008. PubMed ID: 19073330). Functional analysis suggests that the p.Arg386His variant decreases complex I activity (Varghese et al. 2015. PubMed ID: 26345448). Taken together, we classify this variant as likely pathogenic.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 386 of the NDUFV1 protein (p.Arg386His). This variant is present in population databases (rs536758576, gnomAD 0.04%). This missense change has been observed in individual(s) with clinical features of mitochondrial complex I deficiency (PMID: 20818383, 26345448, 35482246). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 496918). 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 NDUFV1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects NDUFV1 function (PMID: 26345448). This variant disrupts the p.Arg386 amino acid residue in NDUFV1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26024641, 29353736, 29948731). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

Published functional studies demonstrate a damaging effect on complex I activity (PMID: 26345448); 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: 28441825, 29976978, 24365713, 25525159, 31665838, 23562761, 27126960, Nurun2021[Article], 34740920, 35586607, 35482246, 35803560, 34807224, 26024641, 25615419, 22644603, 21364701, 28906460, 31324802, 36462614, 26345448, 21696386, 20818383)

The heterozygous p.Arg386His variant in NDUFV1 was identified by our study in the compound heterozygous state, along with another variant of uncertain significance, in 1 individual with mitochondrial complex I deficiency, nuclear type 4. The variant has been reported in 5 individuals of Moroccan and unknown ethnicity with mitochondrial complex I deficiency (PMID: 21696386, 27126960, 20818383), segregated with disease in one affected relative from one family (PMID: 21696386). Of the 5 affected individuals, 2 siblings were homozygotes, which increases the likelihood that the p.Arg386His variant is pathogenic (PMID: 21696386). The p.Arg386His variant has been identified in In 0.03% (19/75000) of African/African American chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs536758576). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID: 496918) as pathogenic by multiple sources. In vitro functional studies provide some evidence that the variant may slightly impact protein function (PMID: 27126960). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The variant is located in a region of NDUFV1 that is essential to protein folding and stability, suggesting that this variant is in a functional domain and slightly supports pathogenicity (PMID: 29976978, 21696386, 23562761). Two additional pathogenic variants, resulting in a different amino acid change at the same position, p.Arg386Leu and p.Arg386Cys, have been reported in association with disease in ClinVar, supporting that a change at this position may not be tolerated (Variation ID: 1465562, 419230). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive mitochondrial complex I deficiency. ACMG/AMP Criteria applied: PP3_moderate, PM5, PM3_supporting, PM1_supporting, PS3_supporting (Richards 2015).