NM_005359.5:c.1081C>A (p.Arg361Ser) in SMAD4 is absent from all population databases (gnomAD v2.1, v4.1, Canada), meeting PM2 (supporting).1 The variant lies in the MH2 domain of SMAD4 at codon 361, a well-established mutational hotspot where multiple pathogenic missense changes (p.Arg361Cys, p.Arg361His, p.Arg361Leu) have been independently reported in patients with juvenile polyposis syndrome and JP-HHT syndrome, meeting PM1 (moderate).2 p.Arg361Ser is a novel missense change at a residue where different pathogenic missense variants are established: p.Arg361Cys (JPS and HHT), p.Arg361His (de novo JPS), and p.Arg361Leu (JP-HHT), meeting PM5 (moderate).3 Multiple in silico tools predict a deleterious effect: REVEL score 0.912 and BayesDel score 0.534, meeting PP3 (supporting).4 SMAD4 is a gene with a well-established role in disease through missense variation, with numerous pathogenic germline missense mutations reported across the MH2 domain and a low rate of benign missense variation, meeting PP2 (supporting).5 This variant has been classified as Likely pathogenic by a clinical diagnostic laboratory (Labcorp Genetics/Invitae; SCV002282679) in ClinVar with criteria provided, meeting PP5 at supporting strength.6 No benign criteria are met. BA1 and BS1 are not satisfied (variant absent from population databases). BP4 is not met (in silico tools predict damaging). BP1 is not applicable (SMAD4 missense variants are a known disease mechanism). BS3 is not met (no evidence of neutral functional effect). Applying generic ACMG/AMP 2015 combination rules: 2 moderate criteria (PM1 + PM5) with supporting evidence (PM2 + PP2 + PP3 + PP5) meets the threshold for Likely Pathogenic. This classification is consistent with the ClinVar record (Likely pathogenic, single submitter).7
SMAD4
Final classification
Likely Pathogenic
SMAD4 c.1081C>A · p.Arg361Ser
SMAD4
NM_005359.5:c.1081C>A (p.Arg361Ser) in SMAD4 is absent from all population databases (gnomAD v2.1, v4.1, Canada), meeting PM2 (supporting).
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 supporting, PM5 moderate, PP2 supporting, PP3 supporting, PP5 supporting; combination = 2 moderate + 4 supporting, which maps to Likely Pathogenic.
Classification rationale
PM1PM2PM5PP2PP3PP5
Likely Pathogenic
SMAD4 c.1081C>A
PM1 + PM2 + PM5 + PP2 + PP3 + PP5
→
Likely Pathogenic
4
revelbayesdel
7
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 · 6 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
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
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Likely pathogenic (1 clinical laboratory). (ClinVarID = 24822)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.14). REVEL score = 0.912. BayesDel score = 0.534117.
Functional
Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-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; COSV61685418, n = 16 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
5papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 4 further PMIDs triaged but not cited — see Sources & References.
Comprehensive analysis of SMAD4 mutations and protein expression in juvenile polyposis: evidence for a distinct genetic pathway and polyp morphology in SMAD4 mutation carriers.
Searched
c.1081C>AR361SArg361Ser1081C>A
Found
Comprehensive analysis of germline SMAD4 mutations in JPS. Reports family AC/AF with a p.Arg361Cys (c.1081C>T) missense mutation, which leads to loss of SMAD4 protein expression in polyps by immunohistochemistry. The specific variant c.1081C>A (p.Arg361Ser) was not identified. Demonstrates that SMAD4 missense mutations at codon 361 are pathogenic and result in protein instability.
Variant
◇ Residue / gene-level — variant not named
Applied to
→PM1 supports · met
→PM5 supports · met
→PP2 supports · met
Why
p.Arg361Cys (not p.Arg361Ser) identified. Used to support PM1 (hotspot), PM5 (different pathogenic missense at same residue), and PP2 (missense mechanism in SMAD4).
Our patient with a germline missense mutation carried an R361C change. This mutation maps to the loop/helix domain in the C-terminal of SMAD4 and has also been found in a sporadic colorectal.
Location Table 2 (family AC/AF: c→t 1083 R361C); Discussion (reference 15: Shi 1997 functional characterization of R361C) · full text
SMAD4 mutations found in unselected HHT patients.
Searched
c.1081C>AR361SArg361Ser1081C>A
Found
Identifies SMAD4 mutations in unselected HHT patients without prior JP diagnosis. Reports c.1081C>T (p.Arg361Cys) in two unrelated HHT patients (5068, 3892) who were subsequently found to have colonic polyps. The specific variant c.1081C>A (p.Arg361Ser) was not identified. Demonstrates that SMAD4 codon 361 missense mutations cause JP-HHT syndrome.
Variant
◇ Residue / gene-level — variant not named
Applied to
→PM1 supports · met
→PM5 supports · met
Why
p.Arg361Cys (not p.Arg361Ser) identified in two patients. Used to support PM1 (hotspot) and PM5 (different pathogenic missense at same residue).
A missense mutation in exon 8 of SMAD4, c.1081C→T, R361C, was found. ... Individual 3892 ... harboured the same SMAD4 exon 8 missense mutation (c.1081C→T, R361C).
Location Results section; Table 1; Figure 1 · full text
High proportion of large genomic deletions and a genotype phenotype update in 80 unrelated families with juvenile polyposis syndrome.
Searched
c.1081C>AR361SArg361Ser1081C>A
Found
Reports mutation and genotype-phenotype analysis in 80 unrelated JPS families. Identifies multiple pathogenic missense changes at SMAD4 codon 361: c.1081C>T (p.Arg361Cys) in patient JUV-87, and c.1082G>A (p.Arg361His) as a de novo mosaic in patient JUV-81. The specific variant c.1081C>A (p.Arg361Ser) was not identified. Establishes a strong genotype-phenotype correlation for gastric polyposis in SMAD4 mutation carriers.
Variant
◇ Residue / gene-level — variant not named
Applied to
→PM1 supports · met
→PM5 supports · met
→PP2 supports · met
Why
p.Arg361Cys and p.Arg361His (not p.Arg361Ser) identified. Used to support PM1 (hotspot), PM5 (different pathogenic missense at same residue), and PP2 (missense mechanism).
Two of the four missense mutations (patients JUV-14 and JUV-78) were proven to have occurred de novo. In a third patient (JUV-81), only a faint mutant signal (c.1082G→A;p.Arg361His) was found during sequencing of exon 8, suggesting that this mutation was present as a mosaic.
Location Table 2 (patients JUV-81 and JUV-87); Results section · full text
Overlapping spectra of SMAD4 mutations in juvenile polyposis (JP) and JP-HHT syndrome.
Searched
c.1081C>AR361SArg361Ser1081C>A
Found
Characterizes the overlapping spectra of SMAD4 mutations in JP and JP-HHT. Reports three different pathogenic missense changes at codon 361: c.1081C>T (p.Arg361Cys) in two JP-HHT patients, c.1082G>T (p.Arg361Leu), and c.1082G>A (p.Arg361His). The specific variant c.1081C>A (p.Arg361Ser) was not identified. Concludes that any SMAD4 mutation can cause JP-HHT and that codon 361 is a recurrent site of pathogenic missense variation.
Variant
◇ Residue / gene-level — variant not named
Applied to
→PM1 supports · met
→PM5 supports · met
→PP2 supports · met
Why
p.Arg361Cys, p.Arg361Leu, and p.Arg361His (not p.Arg361Ser) identified. Used to support PM1 (hotspot), PM5 (different pathogenic missense at same residue), and PP2 (missense mechanism).
Two additional protein-truncating mutations were also identified in exon 2 (MH1 domain) and exon 5 (Linker region). Ten patients harbored missense mutations in exons 8, 9, or 11 encoding the MH2 domain of the protein.
Location Table I (patients 3760, 4138: c.1081C>T p.R361C; 3953: c.1082G>T p.R361L; 4116: c.1082G>A p.R361H); Results section · full text
Mutations in DPC4 (SMAD4) cause juvenile polyposis syndrome, but only account for a minority of cases.
Searched
c.1081C>AR361SArg361Ser1081C>A
Found
Reports a germline missense mutation in SMAD4 at codon 361, specifically c.1081C>T (CGC→TGC, p.Arg361Cys) in a familial JPS patient (AF). This is a different nucleotide and amino acid substitution from c.1081C>A (p.Arg361Ser). The paper demonstrates that germline SMAD4 missense mutations cause JPS and that only a minority of JPS cases are attributable to SMAD4.
Variant
◇ Residue / gene-level — variant not named
Applied to
→PM1 supports · met
→PM5 supports · met
Why
p.Arg361Cys (not p.Arg361Ser) identified. Used to support PM1 (hotspot domain) and PM5 (different pathogenic missense at same residue).
Sequencing (Fig. 2) showed this to result from a missense mutation in codon 361 of DPC4 (CGC→TGC, Arg→Cys).
Location Results (page 1909-1910); Figure 2 · full text
Sources & reference links
Triaged references · 4 PMIDs not cited in assessment
15235019 ↗
The prevalence of MADH4 and BMPR1A mutations in juvenile polyposis and absence of BMPR2, BMPR1B, and ACVR1 mutations.
CLINVAR
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR