rs104894366

chr12-25245284-G-Achr12-25245284-G-Cchr12-25245284-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_004985.5(KRAS):c.101C>T(p.Pro34Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P34R) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KRAS NM_004985.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:7
• Conservation: PhyloP100: 9.98

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 16 ACMG points.

• PM1: In a turn (size 2) in uniprot entity RASK_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_004985.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr12-25245284-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 12590.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.934
• PP5: Variant 12-25245284-G-A is Pathogenic according to our data. Variant chr12-25245284-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 40454.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KRAS	NM_033360.4	c.101C>T	p.Pro34Leu	missense_variant	2/6	ENST00000256078.10
KRAS	NM_004985.5	c.101C>T	p.Pro34Leu	missense_variant	2/5	ENST00000311936.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRAS	ENST00000256078.10	c.101C>T	p.Pro34Leu	missense_variant	2/6	1	NM_033360.4	A1
KRAS	ENST00000311936.8	c.101C>T	p.Pro34Leu	missense_variant	2/5	1	NM_004985.5	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 21, 2012	The P34L missense mutation in the KRAS gene has been reported previously in association with Noonan syndrome (Zenker et al., 2007). Other missense mutations at the same codon (P34Q and P34R) have been reported in association with KRAS-related disorders (Zenker et al., 2007; Schubbert et al., 2006). Therefore, its presence is consistent with a diagnosis of a KRAS-related disorder. The variant is found in NOONAN panel(s). -
Pathogenic, no assertion criteria provided	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Jan 15, 2015	- -

Noonan syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 04, 2013	The Pro34Leu variant in KRAS has not been identified by our laboratory, but has been reported in one individual with Noonan syndrome where it was demonstrated t o have occurred de novo (Zenker 2007). Another variant at the same nucleotide p osition (c.101C>A, p.Pro34Gln) has also been reported in another patient with No onan syndrome where it too, was demonstrated to have occurred de novo (Zenker 20 07). Functional studies have shown that the Pro34Leu variant results in a GTPas e-Activating Protein (GAP)-resistant conformation and consequently, to a weak ga in-of-function, consistent with disease pathogenesis (Gremer 2010). This variant has not been reported in large population studies, consistent with a pathogenic role. Computational analyses (biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) suggest that the variant may impact the protein. In summary, this variant meets our criteria to be classified as pathogenic bas ed on the de novo occurrence and supportive functional studies (http://pcpgm.par tners.org/LMM). -
Pathogenic, reviewed by expert panel	curation	ClinGen RASopathy Variant Curation Expert Panel	Apr 03, 2017	The c.101C>T (p.Pro34Leu) variant in KRAS has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2; PMID 17056636, 20949621). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). A different pathogenic missense variant has been previously identified at this codon of KRAS which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 12590). Computational prediction tools and conservation analysis suggest that the p.Pro34Leu variant may impact the protein (PP3; PMID: 24803665). 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). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PS2, PM2, PM5, PP3, PP2. -

Noonan syndrome 1 Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Molecular Genetics, Centre for Human Genetics

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- -

Noonan syndrome 3 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

3billion

Feb 23, 2023

The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.87; 3Cnet: 0.97). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000040454). The variant has been previously reported as de novo in at least two similarly affected unrelated individuals (PMID: 17056636, 20949621). A different missense change at the same codon (p.Pro34Arg) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000012590). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -

RASopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Mar 09, 2016

This sequence change replaces proline with leucine at codon 34 of the KRAS protein (p.Pro34Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine. This variant is not present in population databases (rs104894366, ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change leads to insensitivity to GTPase-activating protein (GAP) and results in the loss of GAP-induced GTP hydrolysis capability of KRAS. Additional experiments showed  mild increase in the phosphorylation of the downstream targets of KRAS (PMID: 20949621). Two other missense substitution at this codon (p.Pro34Arg and p.Pro34Gln) have also been shown to arise de novo in individuals affected with KRAS-related disorders. The p.Pro34Gln substitution was reported in a patient affected with Noonan syndrome (PMID: 17056636) while the p.Pro34Arg substitution was reported in a patient with cardio-faciocutaneous syndrome (PMID: 16474405). This indicates that the proline residue is important for KRAS protein function. This variant has been shown to arise de novo in individuals affected with Noonan syndrome (PMID: 17056636). ClinVar contains an entry for this variant (Variation ID: 40454). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
Cadd	Pathogenic	31
Dann	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.91	D;D;D;D
M_CAP	Uncertain	0.29	D
MetaRNN	Pathogenic	0.93	D;D;D;D
MetaSVM	Pathogenic	0.85	D
MutationAssessor	Pathogenic	3.2	M;.;M;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.91	D
PROVEAN	Pathogenic	-8.4	D;D;D;D
REVEL	Pathogenic	0.87
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		1.0	D;.;D;.
Vest4		0.95
MutPred		0.77		Gain of catalytic residue at I36 (P = 0.0054);Gain of catalytic residue at I36 (P = 0.0054);Gain of catalytic residue at I36 (P = 0.0054);Gain of catalytic residue at I36 (P = 0.0054);
MVP		0.99
MPC		2.7
ClinPred		1.0	D
GERP RS		5.7
Varity_R		0.97
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs104894366; hg19: chr12-25398218; COSMIC: COSV55588721;