NM_002591.4:c.925G>A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PP3PP5BP4BS2
The NM_002591.4(PCK1):c.925G>A(p.Gly309Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00059 in 1,613,358 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002591.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00103 AC: 157AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00124 AC: 312AN: 250634Hom.: 3 AF XY: 0.00106 AC XY: 144AN XY: 135438
GnomAD4 exome AF: 0.000544 AC: 795AN: 1461016Hom.: 3 Cov.: 31 AF XY: 0.000556 AC XY: 404AN XY: 726768
GnomAD4 genome AF: 0.00103 AC: 157AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74488
ClinVar
Submissions by phenotype
Phosphoenolpyruvate carboxykinase deficiency, cytosolic Pathogenic:4Uncertain:1
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
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This variant is present population databases at a frequency of 0.06% (gnomAD v4.1) has been described as disease-causing in several affected homozygous or compound heterozygous individuals with phosphoenolpyruvate carboxykinase deficiency (e.g. Vieira et al. 2017, PMID: 28216384; Becker et al. 2021, PMID: 33445193). Functional studies have shown that this missense change affects PCK1 function (Vieira et al. 2017, PMID: 28216384). In addition, In silico prediction (REVEL) predicts a deleterious effect for this variant. -
not provided Uncertain:1
This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 309 of the PCK1 protein (p.Gly309Arg). This variant is present in population databases (rs201186470, gnomAD 1.2%). This missense change has been observed in individual(s) with cytosolic phosphoenolpyruvate carboxykinase deficiency (PMID: 28216384, 33445193). ClinVar contains an entry for this variant (Variation ID: 338886). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects PCK1 function (PMID: 28216384). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at