rs757982865
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_002488.5(NDUFA2):āc.134A>Cā(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 (ā ). 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