rs1363497653
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000154.2(GALK1):c.520G>T(p.Glu174*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000154.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1460112Hom.: 0 Cov.: 49 AF XY: 0.00 AC XY: 0AN XY: 726446
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Deficiency of galactokinase Pathogenic:1
NM_000154.1(GALK1):c.520G>T(E174*) is expected to be pathogenic in the context of galactokinase deficiency. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in GALK1, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.