12-25245345-C-T

Position:

• chr12-25245345-C-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PS4_Moderate PS3 PS2 PP2 PP3

This summary comes from the ClinGen Evidence Repository: 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). LINK:https://erepo.genome.network/evrepo/ui/classification/CA156358/MONDO:0018997/004

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: KRAS NM_004985.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:18 O:1
• Conservation: PhyloP100: 7.89

Genes affected

KRAS (HGNC:6407): (KRAS proto-oncogene, GTPase) This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes a protein that is a member of the small GTPase superfamily. A single amino acid substitution is responsible for an activating mutation. The transforming protein that results is implicated in various malignancies, including lung adenocarcinoma, mucinous adenoma, ductal carcinoma of the pancreas and colorectal carcinoma. Alternative splicing leads to variants encoding two isoforms that differ in the C-terminal region. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRAS	NM_033360.4	c.40G>A	p.Val14Ile	missense_variant	2/6	ENST00000256078.10
KRAS	NM_004985.5	c.40G>A	p.Val14Ile	missense_variant	2/5	ENST00000311936.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRAS	ENST00000256078.10	c.40G>A	p.Val14Ile	missense_variant	2/6	1	NM_033360.4	A1
KRAS	ENST00000311936.8	c.40G>A	p.Val14Ile	missense_variant	2/5	1	NM_004985.5	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1460534 Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2 AN XY: 726464

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000334 Hom.: 0

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:18 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2022	KRAS: PM6:Strong, PS3, PM2, PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2021	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) -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 29, 2020	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Molecular Genetics laboratory, Necker Hospital	May 06, 2020	- -

Noonan syndrome 3 Pathogenic:5

Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 01, 2006	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 03, 2019	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pediatrics, Taizhou Central Hospital, Taizhou University Hospital	Feb 01, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	May 22, 2022	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 04, 2016	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. -

Noonan syndrome;C1275081:Cardio-facio-cutaneous syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

May 06, 2014

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. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 05, 2018

- -

Noonan syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen RASopathy Variant Curation Expert Panel

Apr 03, 2017

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). -

RASopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jul 03, 2022

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). -

Noonan syndrome and Noonan-related syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Jul 01, 2018

- -

Endometrial carcinoma Other:1

not provided, no classification provided

literature only

Laboratory of Translational Genomics, National Cancer Institute

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.85
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	28
DANN	Uncertain	1.0
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.94
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.97	D;D;D;D
M_CAP	Uncertain	0.14	D
MetaRNN	Pathogenic	0.84	D;D;D;D
MetaSVM	Pathogenic	0.89	D
MutationAssessor	Pathogenic	3.1	M;.;M;.
MutationTaster	Benign	1.0	A;A;A;A
PrimateAI	Uncertain	0.74	T
PROVEAN	Benign	-0.82	N;N;N;N
REVEL	Pathogenic	0.80
Sift	Uncertain	0.0010	D;D;D;D
Sift4G	Uncertain	0.0060	D;D;D;D
Polyphen		0.98	D;.;D;.
Vest4		0.85
MutPred		0.74		Gain of catalytic residue at G12 (P = 0);Gain of catalytic residue at G12 (P = 0);Gain of catalytic residue at G12 (P = 0);Gain of catalytic residue at G12 (P = 0);
MVP		0.97
MPC		2.5
ClinPred		0.98	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Varity_R		0.88
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs104894365; hg19: chr12-25398279; COSMIC: COSV55501342;