rs544563908
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_000151.4(G6PC1):c.341G>A(p.Gly114Glu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,609,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/22 in silico tools predict a damaging outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. 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. G114A) has been classified as Uncertain significance.
Frequency
Consequence
NM_000151.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PC1 | NM_000151.4 | c.341G>A | p.Gly114Glu | missense_variant, splice_region_variant | 3/5 | ENST00000253801.7 | |
G6PC1 | NM_001270397.2 | c.341-77G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PC1 | ENST00000253801.7 | c.341G>A | p.Gly114Glu | missense_variant, splice_region_variant | 3/5 | 1 | NM_000151.4 | P1 | |
G6PC1 | ENST00000585489.1 | c.341G>A | p.Gly114Glu | missense_variant, splice_region_variant | 3/4 | 5 | |||
G6PC1 | ENST00000592383.5 | c.341-77G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152050Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250724Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135508
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457752Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 725520
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74392
ClinVar
Submissions by phenotype
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Jul 17, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at