rs753571180
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_000154.2(GALK1):c.841G>A(p.Val281Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,596,026 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V281V) has been classified as Likely benign.
Frequency
Consequence
NM_000154.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALK1 | NM_000154.2 | c.841G>A | p.Val281Met | missense_variant | 6/8 | ENST00000588479.6 | |
GALK1 | NM_001381985.1 | c.841G>A | p.Val281Met | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALK1 | ENST00000588479.6 | c.841G>A | p.Val281Met | missense_variant | 6/8 | 1 | NM_000154.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000137 AC: 3AN: 219578Hom.: 0 AF XY: 0.00000822 AC XY: 1AN XY: 121584
GnomAD4 exome AF: 0.0000118 AC: 17AN: 1443796Hom.: 0 Cov.: 34 AF XY: 0.0000125 AC XY: 9AN XY: 717938
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Submissions by phenotype
Deficiency of galactokinase Pathogenic:1Uncertain:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 20, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at