rs575139300
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000154.2(GALK1):c.716G>A(p.Arg239Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,950 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 (★). Synonymous variant affecting the same amino acid position (i.e. R239R) 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 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALK1 | NM_000154.2 | c.716G>A | p.Arg239Gln | missense_variant | 5/8 | ENST00000588479.6 | |
GALK1 | NM_001381985.1 | c.716G>A | p.Arg239Gln | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALK1 | ENST00000588479.6 | c.716G>A | p.Arg239Gln | missense_variant | 5/8 | 1 | NM_000154.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251020Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135794
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461622Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727118
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74488
ClinVar
Submissions by phenotype
Deficiency of galactokinase Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | May 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at