chr3-49022448-C-CT
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_199069.2(NDUFAF3):c.180_181insT(p.Asp61fs) variant causes a frameshift, stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,612,936 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_199069.2 frameshift, stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFAF3 | NM_199069.2 | c.180_181insT | p.Asp61fs | frameshift_variant, stop_gained | Exon 2 of 5 | ENST00000326925.11 | NP_951032.1 | |
NDUFAF3 | NM_199070.2 | c.9_10insT | p.Asp4fs | frameshift_variant, stop_gained | Exon 2 of 5 | NP_951033.1 | ||
NDUFAF3 | NM_199073.2 | c.9_10insT | p.Asp4fs | frameshift_variant, stop_gained | Exon 2 of 5 | NP_951047.1 | ||
NDUFAF3 | NM_199074.2 | c.9_10insT | p.Asp4fs | frameshift_variant, stop_gained | Exon 2 of 5 | NP_951056.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000101 AC: 25AN: 248112Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135156
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1460730Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 726684
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge -
Mitochondrial complex I deficiency Uncertain:1
The p.Asp61X variant in NDUFAF3 has not been previously reported in individuals with mitochondrial complex I deficiency, but has been identified in 0.02% (2/8250) of European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/). This nonsense variant leads to a premature termination codon at position 61, which is predicted to lead to a truncated or absent protein. While complete loss of NDUFAF3 function has been described in a several individuals with mitochondrial complex I deficiency (Saada 2009), the gene-disease association has not been fully established. In summary, while there is some suspicion for a pathogenic role, the clinical significance of the p.Asp61X variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at