3-180984660-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_145261.4(DNAJC19):c.331G>A(p.Glu111Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000618 in 1,455,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E111Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_145261.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC19 | NM_145261.4 | c.331G>A | p.Glu111Lys | missense_variant | Exon 6 of 6 | ENST00000382564.8 | NP_660304.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246178Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133166
GnomAD4 exome AF: 0.00000618 AC: 9AN: 1455622Hom.: 0 Cov.: 29 AF XY: 0.00000414 AC XY: 3AN XY: 724126
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
3-methylglutaconic aciduria type 5 Uncertain:1
This variant has not been reported in the literature in individuals affected with DNAJC19-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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. This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 111 of the DNAJC19 protein (p.Glu111Lys). This variant is present in population databases (rs370042988, gnomAD 0.003%). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at