Starting
Initialising…
0%
KRAS
Final classification
Likely Pathogenic
KRAS c.179G>T · p.Gly60Val
KRAS

NM_033360.3:c.179G>T (p.Gly60Val) is a missense variant in KRAS identified in a single de novo proband with Noonan syndrome and lethal hypertrophic cardiomyopathy (Nosan et al. 2013).

Gene
KRAS
Transcript
NM_033360.3
HGVS · transcript:coding
NM_033360.3:c.179G>T
Consequence
N/A
GRCh38
chr12:25227345 C>A
GRCh37
chr12:25380279 C>A
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KRAS Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule13 (Pathogenic.Moderate >=3) with applied criteria: PS2 moderate, PS4 supporting, PM1 moderate, PM5 moderate, PP3 supporting; maps to Likely Pathogenic.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KRAS Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule13 (Pathogenic.Moderate >=3) with applied criteria: PS2 moderate, PS4 supporting, PM1 moderate, PM5 moderate, PP3 supporting; maps to Likely Pathogenic.
Classification rationale
PS2PS4PM1PM5PP3 Likely Pathogenic
KRAS c.179G>T

NM_033360.3:c.179G>T (p.Gly60Val) is a missense variant in KRAS identified in a single de novo proband with Noonan syndrome and lethal hypertrophic cardiomyopathy (Nosan et al. 2013).1 The variant affects Gly60, which resides in the Switch II domain (AA 57–64), a critical functional domain per RASopathy VCEP specifications (PM1_Moderate).2 At least two different pathogenic missense changes (p.Gly60Ser, p.Gly60Arg) have been reported at the same codon in RASopathy patients, satisfying PM5 at Moderate strength.3 Parental genotyping confirmed the variant occurred de novo, meeting PS2 at Moderate strength (1 de novo point per VCEP rules).4 The variant is observed in a single RASopathy proband, meeting PS4 at Supporting strength (≥1 point per VCEP rules).5 REVEL in silico score of 0.879 exceeds the VCEP threshold of ≥0.7, meeting PP3 at Supporting strength.6 The variant is present at extremely low frequency in gnomAD (v2.1: 1/251,328; v4.1: 3/1,614,068), which is below benign population thresholds but above the PM2 absence requirement.7 Applying the RASopathy VCEP classification rules: three Moderate criteria (PS2_Moderate, PM1, PM5) plus two Supporting criteria (PS4_Supporting, PP3) are met. Per VCEP Rule13, ≥3 Moderate criteria yields a classification of Likely Pathogenic.8

PS2 + PS4 + PM1 + PM5 + PP3 Likely Pathogenic
Gene diagram · NM_033360.3 · variants mapped to exon structure
KRAS NM_033360.3
Fetching transcript structure from UCSC…
Applied criteria · 5 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 1.85866e-06; MAF= 0.00019%, 3/1614068 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54241e-06; MAF= 0.00025%, 3/1179982 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.97886e-06; MAF= 0.00040%, 1/251328 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.79879e-06; MAF= 0.00088%, 1/113652 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00019% · 3 / 1,614,068
      0 hom · FAF 6.8e-05%
      European (non-Finnish)
      3 / 1,179,982
      0.00025%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0004% · 1 / 251,328
      0 hom
      European (non-Finnish)
      1 / 113,652
      0.00088%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (4 clinical laboratories) and as Likely pathogenic (3 clinical laboratories). (ClinVarID = 163766)
      SpliceAI screenshot
      In silico
      SpliceAI predicts possible splice impact for this variant (max delta score = 0.25). REVEL score = 0.879. BayesDel score = 0.303486.
      Functional / OncoKB screenshot
      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.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55708344, n = 5 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & References.
      A lethal course of hypertrophic cardiomyopathy in Noonan syndrome due to a novel germline mutation in the KRAS gene: case study.
      Searched
      c.179G>Tp.Gly60ValG60VGly60Val179G>T
      Found
      A heterozygous missense variant c.179G>T (p.Gly60Val) in KRAS exon 3 was identified as a de novo germline mutation in a preterm infant with Noonan syndrome, dysmorphic features, and rapidly progressive hypertrophic cardiomyopathy leading to death at 4 months of age. The authors note that other mutations at the same residue (p.Gly60Ser, p.Gly60Arg) are known pathogenic NS variants.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PM5 supports · met PS2 supports · met PS4 supports · met
      Why
      Variant-specific germline case with confirmed de novo status; referenced for PS2_Moderate, PS4_Supporting, and PM5_Moderate adjudications.
      This heterozygous unclassified missense variant in exon 3: c.179G>T (p.Gly60Val) might be associated with a lethal form of Noonan syndrome.
      Location Abstract; Case Report, paragraph 2; Discussion, paragraphs 1-2; Figure 2  ·  Context Clinical case report; Sanger sequencing of KRAS coding exons; parental DNA genotyping confirmed de novo status  ·  full text
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      24446311 ↗ BRAF kinase domain mutations are present in a subset of chronic myelomonocytic leukemia with wild-type RAS. ONCOKB
      27288520 ↗ Spectrum and prognostic relevance of driver gene mutations in acute myeloid leukemia. ONCOKB
      34117033 ↗ Clinical and Functional Characterization of Atypical KRAS/NRAS Mutations in Metastatic Colorectal Cancer. ONCOKB
      19396835 ↗ Craniosynostosis in patients with Noonan syndrome caused by germline KRAS mutations. CLINVAR
      30813707 ↗ Provisional Guideline Recommendation for EGFR Gene Mutation Testing in Liquid Samples of Lung Cancer Patients: A Proposal by the Korean Cardiopulmonary Pathology Study Group. CLINVAR
      34958143 ↗ Trio exome sequencing is highly relevant in prenatal diagnostics. CLINVAR
      16474404 ↗ Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome. CLINVAR