KRAS NM_001369786.1:c.40G>A, Val14Ile

The c.40G>A (p.V14I) alteration is located in exon 2 (coding exon 1) of the KRAS gene. This alteration results from a G to A substitution at nucleotide position 40, causing the valine (V) at amino acid position 14 to be replaced by an isoleucine (I). The Genome Aggregation Database (gnomAD) data for this variant is unreliable due to technical and/or biological issues, therefore population frequency estimates were not considered. This variant was reported in individual(s) with features consistent with KRAS-related RASopathy; in at least one individual, it was determined to be de novo (Schubbert, 2006; Zenker, 2007; Nava, 2007; Ko, 2008; Lo, 2009; Ambry internal data). This amino acid position is highly conserved in available vertebrate species. Functional analysis demonstrated that protein containing the p.V14I alteration has an increased rate of the GDP/GTP exchange which resulted in an accumulation of protein in the GTP-bound state and a moderate increase in downstream signaling. In addition, protein with this mutation also showed decrease of binding affinity to RAF1-RBD and RALGDS-RBD (Gremer, 2011). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

Variant summary: c.40G>A affects a conserved nucleotide, resulting in amino acid change from Val to Ile. 3/4 in-silico tools predict this variant to be damaging (SNPs&GO not captured due to low reliability index). This variant was found in 1/102298 control chromosomes at a frequency of 0.0000098, which does not exceed maximal expected frequency of a pathogenic allele (0.0000125). This variant has been reported in multiple NS patients and functional studies showed changes on the GDP/GTP exchange function (dramatic increase of variant both in its intrinsic and GEFcatalyzed nucleotide exchange) as well as impaired RAF-RBD binding ability (Gremer_HM_2011). In addition, multiple clinical laboratories and reputable databases classified this variant as pathogenic. Taken together, this variant was classified as a Pathogenic.

The p.Val14Ile variant in KRAS has been reported in >10 individuals with clinica l features of Noonan syndrome or Cardio-facio-cutaneous syndrome, CFC (Ko 2008, Lo 2008, Gremer 2010, Nava 2007, Schubbert 2006, Zenker 2007, LMM data). This v ariant occurred de novo in at least 5 of these individuals. In addition, functio nal studies show this variant causes a gain-of-function (Schubbert 2006, Gremer 2010), an established pathogenic mechanism in Noonan spectrum disorders. Therefo re, this variant meets our criteria to be pathogenic for Noonan syndrome and CFC in an autosomal dominant manner based on de novo occurrences and functional stu dies.

The variant is not observed in the gnomAD v2.1.1 dataset. It is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. Missense changes are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID:20949621). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.80; 3Cnet: 0.91). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000012589). The variant has been previously reported as de novo in at least two similarly affected unrelated individuals (PMID: 16474405) and observed in at least two similarly affected unrelated individuals (PMID:17704260, 18958496, 19020799, 20949621). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

The c.40G>A variant in the KRAS gene is a missense variant predicted to cause substitution of valine by isoleucine at amino acid 14 (p.Val14Ile). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.803 supporting a deleterious impact to KRAS function (PP3). The variant is located in the KRAS gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2). This variant resides within a region (amino acids 10-17) of KRAS that is defined as a critical functional domain by the ClinGen RASopathy VCEP (PM1). This variant has been reported in 6 individuals with two confirmed de novo occurrences with clinical features of a RASopathy (PS4, PS2_VeryStrong; PMIDs: 16474405, 17704260, 18958496, 19020799, 20949621). In vitro functional studies showed that the p.Val14Ile variant enhanced RAS/MEK/ERK activation (PS3_Moderate; PMID: 20949621). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant RASopathies based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy Variant Curation Expert Panel: PS2_VeryStrong, PS4, PS3_Moderate, PM1, PM2_Supporting, PP2, PP3 (Specification Version 2.3, 12/3/2024)