rs757982865
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_002488.5(NDUFA2):c.134A>C(p.Lys45Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000000688 in 1,452,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. K45K) has been classified as Uncertain significance.
Frequency
Consequence
NM_002488.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFA2 | NM_002488.5 | c.134A>C | p.Lys45Thr | missense_variant | 2/3 | ENST00000252102.9 | |
NDUFA2 | NM_001185012.2 | c.134A>C | p.Lys45Thr | missense_variant | 2/3 | ||
TMCO6 | XM_047417354.1 | c.*513T>G | 3_prime_UTR_variant | 11/11 | |||
NDUFA2 | NR_033697.2 | n.301A>C | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFA2 | ENST00000252102.9 | c.134A>C | p.Lys45Thr | missense_variant | 2/3 | 1 | NM_002488.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247510Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133728
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1452878Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 721320
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Cystic Leukoencephalopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | in vitro;research | MyeliNeuroGene Lab, McGill University Health Center Research Institute | - | This is the first report of autosomal recessive mutations in NDUFA2 associated with cystic leukoencephalopathy. - |
Mitochondrial complex 1 deficiency, nuclear type 13 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 18, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at