Variant classification summary

NM_033360.4:c.40G>A

KRAS · NP_203524.1:p.(Val14Ile) · NM_033360.4

GRCh37: chr12:25398279 C>T · GRCh38: chr12:25245345 C>T

Gene: KRAS Transcript: NM_033360.4

Final call

Pathogenic

PS3 moderate PS4 strong PM1 moderate PM6 moderate PP2 supporting PP3 supporting PP5 supporting

Variant details

Gene

KRAS

Transcript

NM_033360.4

Protein

NP_203524.1:p.(Val14Ile)

gnomAD AF

1.240043996761005e-06 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

The de novo occurrence without confirmed paternity and maternity satisfies PM6 at moderate strength per VCEP criteria.

5

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.

6

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.

7

The ClinGen RASopathy Expert Panel classifies this variant as Pathogenic (ClinVar ID 12589), consistent with the evidence assessment herein.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Pathogenic classification based on the observed combination of very strong, strong, moderate, and supporting pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 is explicitly designated as Not Applicable by the ClinGen RASopathy VCEP (Version 1.0).	cspec
PS1	Not met	No different nucleotide change at codon 14 (Val) has been established as pathogenic per VCEP criteria. No PS1 comparator exists.
PS2	Not met	The VCEP PS2 strong rule requires de novo occurrence with paternity confirmed. PMID 16474405 reports V14I as a de novo germline mutation in Noonan syndrome, but paternity confirmation is not documented in the available abstract and full text is not available. Evidence is assessed under PM6 instead.	PMID:16474405
PS3	Met	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.	PMID:20949621 vcep_svi_rasopathy_vcep_v2_approved_functional_studies
PS4	Met	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 clinvar
PS5	Not assessed	No evidence of the same nucleotide change detected independently or in trans configuration was identified for this variant.
PM1	Met	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_alignment_with_pm1_domains_pptx
PM2	Not met	The VCEP PM2 rule requires the variant to be completely absent from all population databases. gnomAD v4.1 reports 2 alleles out of 1,612,846 (AF = 0.00012%) in the European (non-Finnish) population. Although gnomAD v2.1 and gnomAD-Canada show zero alleles, the presence in gnomAD v4.1 violates the VCEP requirement for complete absence.	gnomad_v4
PM5	N/A	Val14 is within the P-loop, a designated PM1 mutational hotspot. Per VCEP PM5 rule, PM5 should not be used as an independent criterion in conjunction with PM1 when the residue is explicitly designated as a mutational hot-spot. No same-residue pathogenic missense comparator variants were identified.	cspec
PM6	Met	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
PP1	Not met	No segregation data are available for this variant. The VCEP PP1 rule requires at least three informative meioses for the supporting level. No family studies with segregation analysis were identified.
PP2	Met	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.	cspec
PP3	Met	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 bayesdel spliceai
PP4	N/A	PP4 is explicitly designated as Not Applicable by the ClinGen RASopathy VCEP. Proband counting is instead handled under PS4.	cspec
PP5	Met	Expert panel ClinGen RASopathy Variant Curation Expert Panel classified as Pathogenic.	cspec clinvar
BA1	Not met	The VCEP BA1 threshold is allele frequency ≥0.05%. gnomAD v2.1 reports 0/249,502 alleles (AF=0). gnomAD v4.1 reports 2/1,612,846 alleles (AF=0.00012%). Both are well below the 0.05% threshold.	gnomad_v2 gnomad_v4
BS1	Not met	The VCEP BS1 threshold is allele frequency ≥0.025%. The observed frequency in gnomAD v4.1 (0.00012%) is well below this threshold.	gnomad_v2 gnomad_v4
BS2	Not met	The VCEP BS2 rule states that general population data should not be used for this criterion due to variable expressivity and severity in RASopathies. Clinical laboratories are encouraged to accumulate more than 3 instances of well-phenotyped family members before applying. No such evidence is available.
BS3	Not met	VCEP-approved functional studies (PMID 20949621) demonstrate a damaging effect for KRAS V14I, with increased nucleotide exchange, GTP-bound accumulation, and increased downstream signaling. BS3 requires functional studies showing no damaging effect, which is contradicted by the available evidence.	PMID:20949621
BS4	Not met	The VCEP BS4 rule requires only one informative meiosis showing lack of segregation with disease. No such data are available for KRAS V14I.
BP1	N/A	The VCEP BP1 rule applies to truncating variants (nonsense, frameshift, canonical splice sites, initiation codon, entire gene or multi-exon deletion) in genes without established LOF correlation to disease. KRAS V14I (p.Val14Ile) is a missense variant and does not meet the BP1 criteria for truncating variants.	cspec
BP2	Not met	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.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions. NM_033360.4:c.40G>A is a substitution variant.
BP4	Not met	Multiple lines of computational evidence (REVEL 0.803, BayesDel 0.29) suggest a deleterious impact on the gene product. BP4 requires evidence suggesting no impact, which is contradicted by the available in silico data.	revel bayesdel
BP5	Not met	No evidence that this variant has been found in a case with an alternate molecular basis for disease.
BP6	N/A	BP6 is explicitly designated as Not Applicable by the ClinGen RASopathy VCEP per recommendation of the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	N/A	BP7 applies to synonymous (silent) variants or intronic/non-coding variants. NM_033360.4:c.40G>A is a missense variant (p.Val14Ile) and is not eligible for BP7.

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