ClinVar Genomic variation as it relates to human health

The c.40G>A (p.Val14Ile) variant in KRAS has been reported as a confirmed de novo occurrence in at least 2 patients with clinical features of a RASopathy (PS2_VeryStrong; PMID 16474405). The p.Val14Ile variant has been identified in at least 4 independent occurrences in patients with clinical features of a RASopathy (PS4_Moderate; PMID: 20949621, 19020799, 18958496, 17704260). In vitro functional studies provide some evidence that the p.Val14Ile variant may impact protein function (PS3; PMID: 20949621). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of KRAS (PM1; PMID 29493581). 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; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Val14Ile variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PS4_Moderate, PS3, PM1, PP2, PP3).

The KRAS c.40G>A; p.Val14Ile variant (rs104894365) has been reported in several individuals with clinical features of Noonan syndrome, including instances of the variant occurring de novo (Ko 2008, Nava 2007, Schubbert 2006, Zenker 2007). The variant is described as pathogenic by several sources in the ClinVar database (Variation ID: 12589) but is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The valine at codon 14 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. In support of this prediction, experimental studies have shown that this variant results in increased KRAS activity and a mouse model of this variant recapitulates Noonan syndrome (Schubbert 2006, Gremer 2011, Hernandez-Porras 2014). Considering available information, this variant is classified as pathogenic. References: Gremer L et al. Germline KRAS Mutations Cause Aberrant Biochemical and Physical Properties Leading to Developmental Disorders. Hum Mutat. 2011 Jan;32(1):33-43. Hernandez-Porras I et al. K-RasV14I Recapitulates Noonan Syndrome in Mice Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16395-400. Ko JM et al. PTPN11, SOS1, KRAS, and RAF1 gene analysis, and genotype-phenotype correlation in Korean patients with Noonan syndrome. J Hum Genet. 2008;53(11-12):999-1006. Nava C et al. Cardio-facio-cutaneous and Noonan syndromes due to mutations in the RAS/MAPK signalling pathway: genotype-phenotype relationships and overlap with Costello syndrome. J Med Genet. 2007 Dec;44(12):763-71. Schubbert S et al. Germline KRAS mutations cause Noonan syndrome. Nat Genet. 2006 Mar;38(3):331-6. Zenker M et al. Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations. J Med Genet. 2007 Feb;44(2):131-5.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

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.

Published functional studies demonstrate that p.(V14I) results in abnormal KRAS activity (Schubbert et al., 2006; Gremer et al., 2011); The majority of missense variants in this gene are considered pathogenic (HGMD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 24604757, 19020799, 26350204, 20949621, 27174785, 17056636, 17704260, 24803665, 27521173, 27884935, 29948256, 18958496, 30953504, 30050098, 29907801, 31130284, 32960281, 33318624, 17875937, 29493581, 16474405)

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects KRAS function (PMID: 16474405, 17875937, 20949621, 24803665, 25359213). 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) performed at Invitae indicates that this missense variant is expected to disrupt KRAS protein function. ClinVar contains an entry for this variant (Variation ID: 12589). This missense change has been observed in individuals with Noonan syndrome (PMID: 16474405, 17056636, 17704260, 18958496, 19020799). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 14 of the KRAS protein (p.Val14Ile).

KRAS: PM6:Strong, PS3, PM2, PP3

ACMG Criteria: PS2, PS3, PS4, PM1, PM2, PP3, PP5; Variant was found in heterozygous state. De novo-status was confirmed via in-house segregation analysis.

Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is the only reported mechanism of disease in this gene. This gene is associated with multiple somatic and germline conditions. (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from valine to isoleucine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v4) <0.001 for a dominant condition (2 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated RAS domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by an expert panel (ClinVar). (SP) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign