NM_006623.4:c.781G>A
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_006623.4(PHGDH):c.781G>A(p.Val261Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,704 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_006623.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460704Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726698
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
PHGDH deficiency Pathogenic:2Uncertain:1
This sequence change replaces valine with methionine at codon 261 of the PHGDH protein (p.Val261Met). The valine residue is highly conserved and there is a small physicochemical difference between valine and methionine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with phosphoglycerate dehydrogenase deficiency (PMID: 19235232). ClinVar contains an entry for this variant (Variation ID: 3872). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on PHGDH function (PMID: 19235232). 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. -
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Neu-Laxova syndrome 1 Pathogenic:1
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not provided Pathogenic:1
Published functional studies demonstrate a damaging effect and show that this variant affects substrate binding and results in altered enzyme kinetics (Tabatabaie et al., 2009); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 20196394, 19235232) -
not specified Uncertain:1
Variant summary: PHGDH c.781G>A (p.Val261Met) results in a conservative amino acid change located in the D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (IPR006139) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 248336 control chromosomes (gnomAD). c.781G>A has been reported in the literature as a homozygous genotype in at least one individual affected with Phosphoglycerate Dehydrogenase Deficiency (e.g. Tabatabaie_2009 and Coskun_2009). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The variant effect resulted in approximately 22% of normal activity, and reduced substrate affinity (e.g. Tabatabaie_2009). One submitter has provided an assessment for this variant to ClinVar after 2014 without evidence for independent evaluation and classified it as likely pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at