Starting
Initialising…
0%
SMAD4
Final classification
VUS
SMAD4 c.1067C>T · p.Pro356Leu
SMAD4

NM_005359.5:c.1067C>T (p.Pro356Leu) is a missense variant in exon 9 of SMAD4. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, supporting rarity in the general population.

Gene
SMAD4
Transcript
NM_005359.5
HGVS · transcript:coding
NM_005359.5:c.1067C>T
Consequence
N/A
GRCh38
chr18:51065534 C>T
GRCh37
chr18:48591904 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, PP3 supporting; combination = 2 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, PP3 supporting; combination = 2 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2PP3 VUS
SMAD4 c.1067C>T

NM_005359.5:c.1067C>T (p.Pro356Leu) is a missense variant in exon 9 of SMAD4. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, supporting rarity in the general population.1 Residue Pro356 is located in the SMAD4 MH2 domain (aa 324-552), a well-established critical functional domain that mediates SMAD oligomerization and transcriptional activation. This residue additionally lies within a statistically significant mutational hotspot.2 Multiple in silico predictors support a deleterious effect: REVEL score 0.968 (damaging), BayesDel score 0.541 (damaging). SpliceAI predicts no significant splice impact (max delta 0.03).3 This variant has been reported in ClinVar as Uncertain Significance by a single clinical laboratory (Ambry Genetics; ClinVar ID 1782219). It has been observed in 40 somatic cancer samples (COSMIC COSV61685209) and is classified as Likely Oncogenic by OncoKB.4 PVS1 is not applicable (missense variant). In silico evidence meets PP3 (supporting). Population absence meets PM2 (moderate). MH2 domain location and hotspot status meet PM1 (moderate). Verified criteria: PM1 (moderate) + PM2 (moderate) + PP3 (supporting). Under ACMG/AMP 2015 combination rules, 2 moderate + 1 supporting is insufficient for Likely Pathogenic (requires ≥3 moderate, or 2 moderate + ≥2 supporting). No benign criteria are met. PS3 (functional) and PP1 (segregation) were not assessed because variant-specific evidence could not be verified in accessible full-text publications. Overall classification: Uncertain Significance (VUS).5 Gaps: Variant-specific germline functional studies (PS3) and co-segregation data (PP1) were referenced in exploratory literature review (PMID:20101697, PMID:15031030) but could not be verified — abstracts do not mention this variant and full texts are unavailable. Resolution of these gaps could upgrade the classification to Likely Pathogenic.

PM1 + PM2 + PP3 VUS
2 pvs1_gene_context
3 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_005359.5 · variants mapped to exon structure
SMAD4 NM_005359.5
Fetching transcript structure from UCSC…
Applied criteria · 3 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
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 1782219)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.968. BayesDel score = 0.540787.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; 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; COSV61685209, n = 40 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      35101336 ↗ Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). CLINVAR
      20301299 ↗ Heritable Thoracic Aortic Disease Overview. CLINVAR
      22918138 ↗ Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. CLINVAR
      24882528 ↗ Canadian Cardiovascular Society position statement on the management of thoracic aortic disease. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      34131312 ↗ Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
      23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR
      25173340 ↗ 2014 ESC Guidelines on the diagnosis and treatment of aortic diseases: Document covering acute and chronic aortic diseases of the thoracic and abdominal aorta of the adult. The Task Force for the Diagnosis and Treatment of Aortic Diseases of the European Society of Cardiology (ESC). CLINVAR