rs1555559733
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The ENST00000253801.7(G6PC1):āc.361A>Gā(p.Met121Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,116 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M121T) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000253801.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
G6PC1 | NM_000151.4 | c.361A>G | p.Met121Val | missense_variant | 3/5 | ENST00000253801.7 | NP_000142.2 | |
G6PC1 | NM_001270397.2 | c.341-57A>G | intron_variant | NP_001257326.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
G6PC1 | ENST00000253801.7 | c.361A>G | p.Met121Val | missense_variant | 3/5 | 1 | NM_000151.4 | ENSP00000253801 | P1 | |
G6PC1 | ENST00000585489.1 | c.361A>G | p.Met121Val | missense_variant | 3/4 | 5 | ENSP00000466202 | |||
G6PC1 | ENST00000592383.5 | c.341-57A>G | intron_variant | 2 | ENSP00000465958 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461116Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726886
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 05, 2024 | PP3, PM2, PM3, PS3 - |
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 11, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at