19-19516267-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PP3_ModerateBS1_SupportingBS2_Supporting
The NM_015965.7(NDUFA13):āc.29T>Cā(p.Met10Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000223 in 1,613,776 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 Uncertain significance (ā ā ).
Frequency
Consequence
NM_015965.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDUFA13 | ENST00000507754.9 | c.29T>C | p.Met10Thr | missense_variant | Exon 1 of 5 | 1 | NM_015965.7 | ENSP00000423673.1 | ||
ENSG00000258674 | ENST00000555938.1 | c.29T>C | p.Met10Thr | missense_variant | Exon 1 of 7 | 2 | ENSP00000452549.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250680Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135806
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461634Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727120
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:2
This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 10 of the NDUFA13 protein (p.Met10Thr). This variant is present in population databases (rs150011367, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with NDUFA13-related conditions. ClinVar contains an entry for this variant (Variation ID: 2196189). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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Inborn genetic diseases Uncertain:1
The c.29T>C (p.M10T) alteration is located in exon 1 (coding exon 1) of the NDUFA13 gene. This alteration results from a T to C substitution at nucleotide position 29, causing the methionine (M) at amino acid position 10 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at