NM_033360.4:c.40G>A (p.Val14Ile) is located in the P-loop, a critical functional domain of KRAS designated as a PM1 hotspot by the ClinGen RASopathy VCEP.1 Variant-specific functional studies (PMID 20949621) demonstrate that KRAS V14I causes approximately 30-fold increase in nucleotide exchange, accumulation in the GTP-bound state, and increased downstream signaling through MEK, ERK, and AKT. Three VCEP-approved functional assay types (RAS Activation, MEK Activation, ERK Activation) confirm a damaging gain-of-function effect, satisfying PS3 at moderate strength.2 KRAS V14I was first reported as a de novo germline mutation in a patient with Noonan syndrome (PMID 16474405) and has subsequently been identified in at least 5 independent probands across multiple publications, satisfying PS4 at strong strength.3 The de novo occurrence without confirmed paternity and maternity satisfies PM6 at moderate strength per VCEP criteria.4 PP2 applies at supporting strength per VCEP specification that PP2 is applicable to all RASopathy genes. PP3 applies at supporting strength based on REVEL score of 0.803 and multiple lines of computational evidence supporting a deleterious effect.5 This variant is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (2/1,612,846; AF=0.00012%), well below the VCEP BS1 (0.025%) and BA1 (0.05%) thresholds.6 The ClinGen RASopathy Expert Panel classifies this variant as Pathogenic (ClinVar ID 12589), consistent with the evidence assessment herein.7
KRAS
Final classification
Pathogenic
KRAS c.40G>A · p.Val14Ile
KRAS
NM_033360.4:c.40G>A (p.Val14Ile) is located in the P-loop, a critical functional domain of KRAS designated as a PM1 hotspot by the ClinGen RASopathy VCEP.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.0 v1.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 moderate, PS4 strong, PM1 moderate, PM6 moderate, PP2 supporting, PP3 supporting, PP5 supporting; combination = 1 strong + 3 moderate + 3 supporting, which maps to Pathogenic.
Classification rationale
PS3PS4PM1PM6PP2PP3PP5
Pathogenic
KRAS c.40G>A
PS3 + PS4 + PM1 + PM6 + PP2 + PP3 + PP5
→
Pathogenic
1
vcep_alignment_with_pm1_domains_pptx
2
PMID:20949621 ↗vcep_svi_rasopathy_vcep_v2_approved_functional_studies
5
cspec ↗revel
Gene diagram
· NM_033360.4 · variants mapped to exon structure
KRAS
NM_033360.4
Fetching transcript structure from UCSC…
Applied criteria · 7 applied · 12 assessed
Applied · 7
Strength
Supporting
Moderate
Strong
Very strong
✓
PS3
moderate
Pathogenic
Three unique VCEP-approved functional assay types (RAS Activation Assay, MEK Activation Assay, ERK Activation Assay) demonstrate a damaging effect for KRAS V14I. PMID 20949621 directly tested V14I, showing approximately 30-fold increase in nucleotide exchange, accumulation in the GTP-bound state, and increased phosphorylation of MEK, ERK, and AKT. The VCEP supplemental spreadsheet lists V14I as a validated pathogenic control across all three approved assay types. Per VCEP supplemental guidance, two or more unique assay types upgrades PS3 to moderate strength.
RAS Activation Assay (PMID 20949621): V14I listed as pathogenic validation controlincreased GTP-bound RASMEK Activation Assay (PMID 20949621): V14I listed as pathogenic validation control
✓
PS4
strong
Pathogenic
KRAS V14I has been identified in at least 5 independent probands with RASopathy phenotypes across multiple publications and clinical laboratories. PMID 16474405 first reported V14I in Noonan syndrome. Additional probands are documented in PMID 17056636, PMID 17704260, PMID 18958496, and PMID 19020799. The variant has been classified as Pathogenic by 19 clinical laboratories and by the ClinGen RASopathy VCEP (ClinVar ID 12589), further supporting multiple independent occurrences.
PMID 16474405: V14I first discovered in Noonan syndrome probandsPMID 17056636: expanded genotypic spectrum of KRAS germline mutationsPMID 17704260: genotype-phenotype correlation in CFC/NS including KRAS V14I
✓
PM1
moderate
Pathogenic
Val14 is located within the P-loop (phosphate-binding loop), an approved functional domain per the VCEP supplemental PM1 materials (HRAS residues 10-17; homologous in KRAS per Group 1: HRAS, KRAS, NRAS). The P-loop is critical for GTP/GDP binding and is a well-established mutational hotspot in RAS proteins. The variant is absent from population databases at meaningful frequency with no benign variation at this residue.
VCEP PM1 domains document confirms P-loop (residues 10-17) as approved functional domainVal14 is within the P-loopwhich contacts the nucleotide via backbone atoms
✓
PM6
moderate
Pathogenic
PMID 16474405 reports KRAS V14I as a de novo germline mutation in a patient with Noonan syndrome and no family history. Paternity and maternity confirmation are not documented in the available abstract. Per VCEP PM6 moderate rule, confirmed de novo without confirmation of paternity and maternity qualifies at moderate strength.
PMID 16474405: de novo germline KRAS V14I mutation in Noonan syndrome probandpaternity/maternity not confirmed
✓
PP2
supporting
Pathogenic
The VCEP explicitly states that PP2 is applicable to all RASopathy genes described and curated in the framework. KRAS is a RASopathy gene with a low rate of benign missense variation, and missense variants are a common mechanism of disease in RASopathies.
VCEP states PP2 is applicable to all RASopathy genes
✓
PP3
supporting
Pathogenic
Multiple lines of computational evidence support a deleterious effect. REVEL score is 0.803 (pathogenic range). BayesDel score is 0.29 (borderline but consistent with deleterious). SpliceAI predicts no significant splice impact (max delta 0.01). The variant substitutes a highly conserved valine with isoleucine in the P-loop, a critical functional domain.
REVEL score 0.803 (deleterious)BayesDel score 0.289645 (borderline deleterious)SpliceAI max delta 0.01 (no splicing impact)
Assessed · not applied
Pathogenic
PS1
No different nucleotide change at codon 14 (Val) has been established as pathogenic per VCEP criteria.
PS2
The VCEP PS2 strong rule requires de novo occurrence with paternity confirmed.
PM2
The VCEP PM2 rule requires the variant to be completely absent from all population databases.
PP1
No segregation data are available for this variant.
Benign
BA1
The VCEP BA1 threshold is allele frequency ≥0.05%.
BS1
The VCEP BS1 threshold is allele frequency ≥0.025%.
BS2
The VCEP BS2 rule states that general population data should not be used for this criterion due to variable expressivity and severity in RASopathies.
BS3
VCEP-approved functional studies (PMID 20949621) demonstrate a damaging effect for KRAS V14I, with increased nucleotide exchange, GTP-bound accumulation, and increased downstream signaling.
BS4
The VCEP BS4 rule requires only one informative meiosis showing lack of segregation with disease.
BP2
No evidence of this variant observed in trans with a pathogenic variant for a fully penetrant dominant disorder or in cis with a pathogenic variant in any inheritance pattern.
BP4
Multiple lines of computational evidence (REVEL 0.803, BayesDel 0.29) suggest a deleterious impact on the gene product.
BP5
No evidence that this variant has been found in a case with an alternate molecular basis for disease.
N/A · 7
PVS1 · PM5 · PP4 · BP1 · BP3 · BP6 · BP7
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.24004e-06; MAF= 0.00012%, 2/1612846 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.69593e-06; MAF= 0.00017%, 2/1179292 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/249502 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16070 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00012%
· 2 / 1,612,846
0 hom · FAF 2.8e-05%
0 hom · FAF 2.8e-05%
European (non-Finnish) 2 / 1,179,292 |
0.00017% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent
· 0 / 249,502
0 hom
0 hom
Not observed in any ancestry group.
+ 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Pathogenic (19 clinical laboratories) and as pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen RASopathy Variant Curation Expert Panel (expert panel). (ClinVarID = 12589)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.803. BayesDel score = 0.289645.
Functional
Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
COSMIC
Cancer hotspots
Somatic evidence
Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55501342, n = 46 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
3papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 5 further PMIDs triaged but not cited — see Sources & References.
Germline KRAS mutations cause Noonan syndrome.
Searched
V14IVal14c.40G>A
Found
First report of germline KRAS mutations in Noonan syndrome. V14I, T58I, and D153V were identified as de novo heterozygous mutations in PTPN11 mutation-negative Noonan syndrome patients. V14I and T58I reduce GTPase activity, resulting in increased RAS signaling.
Variant
✓ Names this variant
Applied to
→PM6 supports · met
→PS4 supports · met
Why
De novo occurrence reported without paternity/maternity confirmation; supports PM6 at moderate and contributes to PS4 proband count.
We discovered de novo germline KRAS mutations that introduce V14I, T58I or D153V in five PTPN11-negative individuals with Noonan syndrome.
Location Abstract
Noonan syndrome and related disorders: dysregulated RAS-mitogen activated protein kinase signal transduction.
Searched
V14IVal14c.40G>A
Found
Review article discussing KRAS mutations in Noonan syndrome. Summarizes that V14I and T58I mutant KRAS proteins in the P-loop and Switch II have less GTPase activity than wild-type KRAS but more than oncogenic G12D, reducing RAS inactivation and resulting in increased signaling.
Variant
✓ Names this variant — characterised directly
Applied to
→PS4 supports · met
Why
Review article; does not provide primary variant-specific data. Confirms V14I in RASopathy context. Not independently cited for functional evidence.
Two mutant KRAS proteins, V14I and T58I, affecting the P-loop and Switch II in the G domain, respectively, have less GTPase activity, basally and after stimulation with a GAP protein, than wild-type KRAS but more than the oncogenic G12D.
Location New Noonan syndrome gene discovery–KRAS section, paragraph 3 · full text
Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders.
Searched
V14IVal14c.40G>AV14
Found
Comprehensive biochemical characterization of 10 germline KRAS mutants including V14I. KRAS V14I demonstrated approximately 30-fold increase in intrinsic and GEF-catalyzed nucleotide exchange, accumulation in GTP-bound active state in COS-7 cells, and increased phosphorylation of MEK, ERK, and AKT. Classified as Class B mutant with fast nucleotide exchange as the primary pathogenic mechanism.
Variant
✓ Names this variant — characterised directly
Applied to
→PS3 supports · met
Why
Variant-specific functional data confirmed in three VCEP-approved assay types (RAS, MEK, ERK activation); referenced in PS3 assessment at moderate strength.
The most significant effect was an increase in dissociation of the fluorescently labeled GDP (mantGDP) from RAS mutants by almost 30-fold in the case of p.V14I and p.Q22E, and more than 60-fold in p.F156L.
Location Results throughout; Table 1; Figures 2-5; Discussion Class B · Context COS-7 cells transiently transfected with KRAS variants; recombinant HRAS proteins expressed in E. coli; GST pull-down assays using RAF1-RBD; fluorescence-based nucleotide exchange and GTP hydrolysis assays · full text
Sources & reference links
9Sources
Triaged references · 5 PMIDs not cited in assessment
34117033 ↗
Clinical and Functional Characterization of Atypical KRAS/NRAS Mutations in Metastatic Colorectal Cancer.
ONCOKB
25173338 ↗
2014 ESC Guidelines on diagnosis and management of hypertrophic cardiomyopathy: the Task Force for the Diagnosis and Management of Hypertrophic Cardiomyopathy of the European Society of Cardiology (ESC).
CLINVAR