The SMAD4 NM_005359.6:c.1082G>A (NP_005350.1:p.(Arg361His)) missense variant has previously been reported in somatic cancers (COSMIC; COSV61684056, n = 261 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: Two variant-specific recombinant-protein assays consistently found that SMAD4 R361H disrupted or completely abolished Smad2-Smad4 complex formation. Based on available guidelines, this variant is considered to be Pathogenic.
Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
Pathogenic.A pathogenic classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.SMAD4 encodes a protein that helps transmit TGF-beta and bone morphogenetic protein signals to the nucleus, where it controls genes involved in cell growth and tissue development. It acts as a tumor suppressor and is associated with juvenile polyposis syndrome and hereditary hemorrhagic telangiectasia. Loss or alteration of SMAD4 is especially linked to pancreatic cancer and can also occur in colorectal and lung cancers.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, strong: two variant-specific recombinant-protein assays consistently found that SMAD4 R361H disrupted or completely abolished Smad2-Smad4 complex formation.
Met at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, corresponding to frequency 0, below the PM2 threshold of <=0.0001.
Met, strong: missense REVEL score 0.955 meets the PP3 strong threshold of >=0.932.
No benign criterion marked as applied in the recorded assessment.
Pathogenic: PS3 (strong) and PP3 (strong), with PM2 (supporting), satisfy the generic ACMG/AMP rule for two strong pathogenic criteria.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
Recorded REVEL score: 0.955. Refer to the recorded PP3/BP4 rationale for interpretation.
6 Pathogenic · 1 Likely pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV61684056, n = 261 times).
This variant lies in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 3 met · 6 not met · 14 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The SMAD4 VCEP is listed without released criteria, so the supplied generic ACMG/AMP rules govern.
No qualifying case-control prevalence estimate, patient-specific phenotype, alternate molecular basis, or exact-variant expert-panel classification was identified for these five criteria.
The variant is missense, so PP3 and BP4 use the REVEL path only; the same REVEL result is not double-counted between criteria.
REVEL 0.955 supports PP3 at strong strength and does not support BP4.
No criteria match.
PS3 is met at strong strength. Two independent, variant-specific biochemical studies evaluated SMAD4 p.Arg361His using recombinant protein constructs and appropriate comparator mutations/controls. Wu et al. assessed purified SMAD4 and SMAD2 domains by size-exclusion chromatography and related biophysical analyses, reporting that R361H disrupted Smad2-Smad4 heterocomplex formation while evaluating protein folding and solution properties. Shi et al. used a recombinant phosphorylated Smad2-Smad4 MH2-domain gel-filtration assay and reported that R361H completely abolished complex formation, whereas a comparator SMAD4 mutation had no detectable effect. These orthogonal, biologically relevant assays directly test the SMAD4 interaction required for TGF-beta signaling and consistently demonstrate loss of function for the exact variant. The evidence is strong functional support, although the bundle does not document validation in a clinical diagnostic laboratory setting.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
PM2 is met at supporting strength. NM_005359.6:c.1082G>A is absent from gnomAD v2.1 and gnomAD v4.1, and the available non-cancer subset entries also report absence. This satisfies the generic PM2 population requirement; under the supplied ClinGen SVI default, PM2 is supporting and the <=0.0001 threshold is met by an observed allele count of zero.
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
The variant is a missense substitution, NM_005359.6:c.1082G>A (p.Arg361His), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for PP3/BP4 here. REVEL is 0.955, meeting the generic PP3 strong threshold of >= 0.932 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
PP3: Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (strong): >= 0.932 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
PP5 requires a reputable recent report of the exact variant as pathogenic when the supporting evidence is unavailable for independent evaluation. The exact-variant ClinVar record is Pathogenic/Likely pathogenic, but the audit documents 0 expert-panel submissions and only clinical-laboratory submissions; under the specified generic rule, these assertions do not qualify for PP5.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BA1 is not met. NM_005359.6:c.1082G>A (SMAD4 p.Arg361His) was absent from gnomAD v2.1 and gnomAD v4.1, as well as the available non-cancer subsets; therefore no allele frequency or grpmax FAF approaches the generic BA1 threshold of >=0.05. No population-frequency evidence supports a stand-alone benign call.
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
BS1 is not met. The variant is absent from gnomAD v2.1 and v4.1, including the available non-cancer subset entries, so there is no observed population frequency or grpmax FAF >=0.01. The absence provides no evidence that the allele frequency is greater than expected for SMAD4-related disease.
Allele frequency is greater than expected for disorder.
BS3 is not met because the available variant-specific functional evidence does not show a lack of damaging effect. Instead, two recombinant-protein studies directly evaluated SMAD4 p.Arg361His and reported disrupted or completely abolished Smad2-Smad4 heterocomplex formation, a biologically relevant function of the SMAD4 protein. No exact-variant assay in the reviewed evidence demonstrates normal protein function or normal splicing.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The variant is a missense substitution, so BP4 must be assessed using REVEL only. REVEL is 0.955, which is above rather than at or below the strongest generic BP4 threshold of <= 0.016 and also exceeds the supporting threshold of <= 0.29; therefore BP4 is not met. The SpliceAI max delta of 0.079 is not considered because splice prediction is not the applicable path for a missense variant.
BP4: Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BP6 requires a reputable recent report of the exact variant as benign when the supporting evidence is unavailable for independent evaluation. The exact-variant ClinVar audit contains no benign expert-panel classification and instead records Pathogenic/Likely pathogenic clinical-laboratory submissions, so the specified generic PP5/BP6 rule does not permit BP6.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The variant is p.Arg361His (c.1082G>A), and the reviewed literature documents this exact amino-acid change, but no evidence identifies a previously established pathogenic p.Arg361His caused by a different nucleotide change. The available ClinVar record is for the same c.1082G>A allele, not an alternate nucleotide change at codon 361. The caveat about splice effects is not limiting here because the variant is annotated as missense and SpliceAI's maximum delta score is 0.079.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
No case-specific evidence documents that NM_005359.6:c.1082G>A (SMAD4 p.Arg361His) is de novo, and no confirmed maternity and paternity results are provided. The available literature and case records do not establish both parental relationships, absence of the variant in both parents, a disease phenotype in the proband, or absence of family history. Therefore, PS2 cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
The governing PS4 definition requires a significantly increased prevalence in affected individuals versus controls; Note 1 specifies OR or RR >5.0 with a confidence interval excluding 1.0. The reviewed literature identifies SMAD4 p.Arg361His in affected or tumor-derived reports, including PMID:15014009 Table 2 and PMID:11274206, but provides no matched control count, case/control frequency comparison, OR/RR, or 95% confidence interval for this exact variant. The papers listed as PS4 candidates in literature_pass.json were checked through the available extracts and literature metadata; they do not establish the required case-control comparison. Because the required comparison cannot be calculated, PS4 is not assessed rather than inferred from repeated case reports.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
SMAD4 p.Arg361His lies in the MH2-domain mutational cluster region reported as codons 330-370, and biochemical studies place R361H in the loop-helix region important for Smad2-Smad4 interaction. However, the generic PM1 definition also requires that the hotspot or critical domain be without benign variation, and the available evidence does not establish that condition across the relevant region. The SMAD4 VCEP record has no released criteria and vcep_materials.json has no domain_tables entry, so no authoritative gene-specific domain list or PM1 rule resolves this missing requirement.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
The queried variant changes Arg361 to His. The reviewed evidence documents R361H itself, but no different missense substitution at residue 361 with an established pathogenic classification was identified. Reported D351H and V370D variants are at different residues and therefore do not satisfy PM5.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
No case-specific evidence documents an assumed de novo occurrence of NM_005359.6:c.1082G>A (SMAD4 p.Arg361His). The available records do not report the variant in the proband relative to either parent, nor do they establish whether parental testing was absent or incomplete. Therefore, PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
No case-specific pedigree or testing data document co-segregation of NM_005359.6:c.1082G>A (SMAD4 p.Arg361His) with disease in affected family members. The literature includes reports of other SMAD4 variants and general SMAD4-related disease cohorts, but those data do not establish segregation of this exact variant in this family. Therefore, PP1 cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.
The evidence supports SMAD4 loss of function as a disease mechanism, but it does not establish both PP2 requirements: a low rate of benign missense variation and missense variants being a common disease mechanism. No gene-level benign-missense-rate metric or qualifying comparative dataset was supplied for SMAD4.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
The governing PP4 definition requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. The case evidence identifies SMAD4 and the associated juvenile polyposis/hereditary hemorrhagic telangiectasia disease context, but does not provide this patient's phenotype, family history, or a sufficiently specific clinical presentation. General disease descriptions and literature-level syndrome statements cannot substitute for the patient's phenotype.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 is not assessed. The population evidence shows absence from gnomAD v2.1 and v4.1 but does not document an individual-level observation of this variant in a healthy adult, a homozygote, a heterozygote, or a hemizygote. A population-database absence cannot establish the healthy-adult observation required for BS2.
BS2
No case-specific evidence documents affected family members who were tested and found not to carry NM_005359.6:c.1082G>A (SMAD4 p.Arg361His). The available records do not provide a pedigree, affected-relative genotypes, or phenotype adjudication sufficient to evaluate non-segregation, and no conclusion can be drawn from the absence of family data. Therefore, BS4 cannot be assessed.
Lack of segregation in affected members of a family. ... Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals.
The available gene-context evidence supports loss of function as a SMAD4 disease mechanism, but it does not demonstrate that primarily truncating variants, rather than missense variants, are known to cause disease. The supplied evidence lacks a systematic variant-spectrum comparison sufficient for BP1.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
BP2 cannot be assessed from the available evidence. Although the CSPEC disease framework identifies SMAD4-related juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome as autosomal dominant, no pathogenic variant in trans or cis with NM_005359.6:c.1082G>A (p.Arg361His), and no parent/offspring phase testing, is documented. The required fully penetrant dominant-disease condition is also not established in the case evidence.
BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
BP5 requires the variant to be found in a case with an alternate molecular basis for disease. The available evidence reports SMAD4 p.Arg361His in affected or tumor-derived contexts and functional studies, but does not document an affected case with a different molecular diagnosis that explains the disease instead of this variant.
Variant found in a case with an alternate molecular basis for disease.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_005359.6:c.1082G>A in SMAD4 is a missense substitution predicted to produce NP_005350.1:p.(Arg361His). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for SMAD4, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
PM3 is not applicable because the available disease framework identifies SMAD4-related juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome as autosomal dominant, whereas PM3 applies to recessive disorders. No recessive SMAD4 interpretation is supported for this case.
PM3: For recessive disorders, detected in trans with a pathogenic variant
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_005359.6:c.1082G>A in SMAD4 is a missense substitution predicted to produce NP_005350.1:p.(Arg361His). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for SMAD4, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_005359.6:c.1082G>A in SMAD4 is a missense substitution predicted to produce NP_005350.1:p.(Arg361His). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for SMAD4, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_005359.6:c.1082G>A in SMAD4 is a missense substitution predicted to produce NP_005350.1:p.(Arg361His). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for SMAD4, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in SMAD4, mapped onto the exon structure of NM_005359.6. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
The variant is a missense substitution, NM_005359.6:c.1082G>A (p.Arg361His), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for PP3/BP4 here. REVEL is 0.955, meeting the generic PP3 strong threshold of >= 0.932 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997).
PP3: Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (strong): >= 0.932 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
The variant is a missense substitution, so BP4 must be assessed using REVEL only. REVEL is 0.955, which is above rather than at or below the strongest generic BP4 threshold of <= 0.016 and also exceeds the supporting threshold of <= 0.29; therefore BP4 is not met. The SpliceAI max delta of 0.079 is not considered because splice prediction is not the applicable path for a missense variant.
BP4: Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_005359.6:c.1082G>A in SMAD4 is a missense substitution predicted to produce NP_005350.1:p.(Arg361His). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for SMAD4, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08). REVEL score = 0.955. BayesDel score = 0.578234.
7 paper records listed. 2 cited in the classification.
Each of the three tumor-derived mutations in Smad4 (D351H, R361H, and V370D), as well as their corresponding mutations in Smad2 (D300H, R310H, and V319D), disrupted the formation of a heterocomplex (Table II; Fig. 4A).
Location Results and Discussion, ‘Tumorigenic Mutations Disrupt the Formation of the Smad2-Smad4 Heterodimer’; Table II
Context Recombinant Smad4 residues 251-552 and Smad2 residues 241-467 were expressed in E. coli, purified, and assessed for heterocomplex formation using size-exclusion chromatography and related biochemical analyses.
Two mutations affecting residues in the loop-helix region of Smad4, D351H and R361H, completely abolished the formation of the Smad2-Smad4 complex, whereas D537H in the helix-bundle region of Smad4 had no detectable effect (Table 2).
Location Results, ‘Mutational Analysis’; Table 2; Discussion, ‘Tumor-Derived Mutations’
Context Recombinant phosphorylated Smad2 MH2 domain and Smad4 MH2 domain were analyzed for heterocomplex formation by gel filtration.
Colorectal cancer 361 CGC to CAC 22, 41, and 42
Table 2, Colorectal cancer section; Results, ‘Mapping of Mutations and Identification of the Mutational Hot Spots of MADH4’; Discussion
Mutations in the SMAD4 gene can cause a rare syndrome which combines juvenile polyposis and HHT.
Diagnosis of HHT, Background; recommendations section on genetic testing
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (6 clinical laboratories) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 24832)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08). REVEL score = 0.955. BayesDel score = 0.578234.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV61684056, n = 261 times).
This variant lies in a statistically significant hotspot.