11-66870399-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_001040716.2(PC):c.806G>A(p.Arg269Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,461,476 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).
Frequency
Consequence
NM_001040716.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PC | NM_001040716.2 | c.806G>A | p.Arg269Gln | missense_variant | Exon 9 of 23 | ENST00000393960.7 | NP_001035806.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250722Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135656
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461476Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727076
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Pyruvate carboxylase deficiency Pathogenic:4Uncertain:2
Variant summary: PC c.806G>A (p.Arg269Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 250722 control chromosomes. c.806G>A has been reported in the literature in bi-allelic individuals affected with Pyruvate Carboxylase Deficiency Type A and B, with PC activity in cultured skin fibroblasts below reference range (examples: Wang_2008 and Lasio_2023). These data indicate that the variant is likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 18676167, 37207470). ClinVar contains an entry for this variant (Variation ID: 550614). Based on the evidence outlined above, the variant was classified as pathogenic. -
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This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 269 of the PC protein (p.Arg269Gln). This variant is present in population databases (no rsID available, gnomAD 0.002%). This missense change has been observed in individual(s) with pyruvate carboxylase deficiency (PMID: 18676167). ClinVar contains an entry for this variant (Variation ID: 550614). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PC protein function. 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. -
The observed missense c.806G>A(p.Arg269Gln) variant in PC gene has been reported previously in homozygous state in individuals affected with pyruvate carboxylase deficiency (Wang D, et al., 2008; Bayat R, et al., 2021). The p.Arg269Gln variant has been reported with allele frequency of 0.0008% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Uncertain Significance / Likely Pathogenic. The amino acid change p.Arg269Gln in PC is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 269 is changed to a Gln changing protein sequence and it might alter its composition and physico-chemical properties. However, additional functional studies will be required to prove the pathogenicity of this variant. For these reasons, this variant has been classified as Likely Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at