Variant classification summary

NM_005359.5:c.1081C>G

SMAD4 · NP_005350.1:p.(Arg361Gly) · NM_005359.5

GRCh37: chr18:48591918 C>G · GRCh38: chr18:51065548 C>G

Gene: SMAD4 Transcript: NM_005359.5

Final call

Pathogenic

PS2 strong PS4 moderate PM1 moderate PM2 moderate PP3 supporting PP4 supporting

Variant details

Gene

SMAD4

Transcript

NM_005359.5

Protein

NP_005350.1:p.(Arg361Gly)

gnomAD AF

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

De novo occurrence confirmed in a proband with juvenile polyposis and hereditary hemorrhagic telangiectasia overlap syndrome; variant absent from both unaffected parents with paternity and maternity confirmed by haplotype analysis.

2

Observed in at least 2-3 unrelated probands with juvenile polyposis syndrome, representing a significantly increased prevalence in affected individuals compared to the general population.

3

Located within the MH2 domain (Mutational Rich Region 1), a well-established functional domain and statistically significant mutational hotspot in SMAD4.

4

Absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, with allele frequency of zero in all populations.

5

REVEL score of 0.885 strongly predicts a deleterious effect; SpliceAI confirms no cryptic splice alteration (max delta 0.05), consistent with a missense mechanism.

6

Proband phenotype (colonic juvenile polyps, anemia, telangiectases, epistaxis) is highly specific for the SMAD4-associated JP-HHT overlap syndrome.

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	Variant is a missense substitution (c.1081C>G, p.Arg361Gly) and does not fall into null-variant categories (nonsense, frameshift, or canonical ±1,2 splice site). Per ClinGen SVI PVS1 recommendations (PMC6185798), the generic PVS1 framework is not applicable.	pvs1_generic_framework
PS1	Not assessed	No alternative nucleotide change at c.1081 yielding the same amino acid substitution (p.Arg361Gly) has been identified in the literature or variant databases. PS1 requires a different nucleotide change at the same position producing the same amino acid change, already established as pathogenic.
PS2	Met	De novo occurrence confirmed in a proband with juvenile polyposis and hereditary hemorrhagic telangiectasia (JP-HHT overlap syndrome). The variant (c.1081C>G, p.Arg361Gly) was absent from both unaffected parents in Family 230. Chromosome 18 haplotype analysis confirmed biological parentage (PMID:15031030). Phenotype is highly specific for SMAD4-related disease.	PMID:15031030
PS3	Not met	No variant-specific functional assay has been performed for NM_005359.5:c.1081C>G (p.Arg361Gly). PMID:22316667 studied the functional impact of SMAD4 mutations on BMP signaling but assessed c.1081C>A (p.Arg361Ser), not c.1081C>G. OncoKB curation of Likely Oncogenic / Likely Loss-of-function is a literature-derived inference, not direct experimental evidence for this variant.	PMID:22316667
PS4	Met	The variant has been observed in at least 2-3 unrelated probands with juvenile polyposis syndrome (JPS) and/or JPS-HHT overlap syndrome. PMID:15031030 reports c.1081C>G de novo in Family 230 (JP/HHT). PMID:18823382 lists c.1081C>G (R361G) in sporadic proband JP71 with JPS. PMID:22316667 confirms two patients in the JP database shared substitutions at nucleotide 1081. Observed prevalence in affected individuals is significant given the rarity of JPS.	PMID:15031030 PMID:18823382 PMID:22316667
PS5	N/A	PS5 (different nucleotide change at the same position resulting in a different amino acid change, known to be pathogenic) is not a criterion in the ACMG/AMP 2015 standard framework and does not appear in the generic ACMG classification rules used for this case.
PM1	Met	Located in a well-established functional domain and a statistically significant mutational hotspot. The variant lies within the MH2 domain (codons 323-552) and specifically within Mutational Rich Region 1 (MRR1, codons 330-370), the most frequently mutated region of SMAD4. The MH2 domain mediates protein-protein interactions with R-SMADs and transcriptional activity (PMID:18823382). Hotspot analysis confirmed statistical significance at this residue.	PMID:18823382
PM2	Met	Absent from all population databases. No allele count observed in gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), or gnomAD-Canada v1.0 (genomes). Allele frequency is 0.00, well below the PM2 threshold of <0.1%.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 candidate harvesting could not confirm classic same-residue comparator variants suitable for PM5 application. While c.1081C>A (p.Arg361Ser) exists at the same residue, it has not been established as pathogenic through functional or clinical evidence (PMID:22316667 demonstrated only 8% reduction in BMP signaling, not statistically significant). The pm5_candidates pipeline also returned no eligible comparators.	pm5_candidates PMID:22316667
PM6	N/A	The confirmed de novo event has been applied at the strong level under PS2 (paternity and maternity confirmed by haplotype analysis, PMID:15031030). PM6 (assumed de novo without confirmed parentage) addresses a lower evidence tier that has been superseded by the confirmed de novo observation. No additional unconfirmed de novo reports exist for this variant.	PMID:15031030
PP1	Not assessed	Limited cosegregation data are available. The variant occurred as a de novo event in a single proband (Family 230, PMID:15031030) with no additional affected family members to evaluate cosegregation. No multi-generation pedigree with segregation analysis has been published for this variant.	PMID:15031030
PP2	Not assessed	HCI prior scores are not available for SMAD4 (gene not supported by the HCI prior database). PP2 requires demonstration that missense variants are a common mechanism of disease in a gene with a low rate of benign missense variation, typically assessed via the HCI prior or gene-level Z-score. Without HCI prior data, this criterion cannot be formally applied.
PP3	Met	Multiple lines of computational evidence support a deleterious effect. REVEL score 0.885 (strongly damaging, well above 0.75 threshold). The variant lies within the highly conserved MH2 domain at a residue within a statistically significant mutational hotspot. SpliceAI predicts no cryptic splice impact (max delta 0.05), consistent with a pure missense mechanism. BayesDel score 0.512 provides additional, though weaker, supporting evidence.	revel bayesdel spliceai
PP4	Met	The phenotype of the proband harboring this variant is highly specific for SMAD4-related disease. The affected individual (PMID:15031030, Family 230, II-2) presented with both juvenile polyposis (multiple colonic polyps, anemia) and hereditary hemorrhagic telangiectasia (telangiectases, epistaxis), the characteristic JP-HHT overlap syndrome specifically associated with SMAD4 mutations rather than ENG or ACVRL1 mutations.	PMID:15031030
PP5	Not assessed	ClinVar classifies this variant as Pathogenic (Variation ID 24830; 2 clinical laboratories, criteria provided, single submitter). However, PP5 is intended for cases where a reputable source has reported the variant as pathogenic but the evaluating laboratory lacks access to the underlying evidence. In this assessment, all available evidence has been independently evaluated at the criteria level, making PP5 redundant.	clinvar
BA1	Not met	Variant is absent from all population databases including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Allele frequency is 0.00, well below the BA1 threshold of >1% (non-VCEP).	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	Variant is absent from all population databases. Allele frequency is 0.00, below the BS1 threshold of >0.3% (non-VCEP).	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	Variant is absent from population databases. No observation in healthy adult controls to suggest this variant occurs in the general population without disease. JP/HHT is an adult-onset disorder with age-dependent penetrance, but zero population observations do not support BS2.	gnomad_v2 gnomad_v4 gnomad_canada
BS3	Not met	No well-established functional studies demonstrate a neutral or benign effect. The only functional study at the same residue (c.1081C>A, p.Arg361Ser, PMID:22316667) showed an 8% reduction in BMP signaling that was not statistically significant, but this does not constitute evidence of a benign effect for c.1081C>G. The somatic observation of R361G as a stable mutation in ovarian low-grade serous carcinoma (PMID:25523272) is consistent with a functional role in tumorigenesis.	PMID:22316667 PMID:25523272
BS4	Not met	No evidence of non-segregation with disease. The only family data available (PMID:15031030) shows the variant arose de novo in an affected proband with no affected relatives, which does not provide non-segregation evidence.	PMID:15031030
BP1	Not met	Although BP1 is intended for missense variants in genes where truncating variants are the primary mechanism of disease, missense variants in the MH2 domain of SMAD4 are a well-established pathogenic mechanism in JPS and JP-HHT. Multiple pathogenic missense variants in this domain have been reported (PMID:18823382, PMID:15031030).	PMID:18823382 PMID:15031030
BP2	Not met	No observation of this variant in trans with a known pathogenic SMAD4 variant. SMAD4-related disorders (JPS, HHT, JP-HHT) are autosomal dominant with hapoinsufficiency as the disease mechanism; observation in trans is not expected and BP2 does not apply.
BP3	N/A	Variant is a missense substitution; BP3 applies to in-frame deletions or insertions in repetitive regions.
BP4	Not met	Multiple in silico tools predict a deleterious effect. REVEL score 0.885 is strongly in the damaging range (>0.75). SpliceAI predicts no splice impact (max delta 0.05), which is consistent with a missense mechanism rather than a benign indication. Computational evidence supports pathogenicity, not a benign interpretation.	revel bayesdel spliceai
BP5	Not met	No observation of this variant in a case with an alternate molecular basis for disease. The variant has been reported exclusively in probands with SMAD4-related phenotypes (JPS, JP-HHT).	PMID:15031030 PMID:18823382
BP6	Not met	ClinVar classifies this variant as Pathogenic (Variation ID 24830), not Benign or Likely Benign. BP6 requires a reputable source to classify the variant as benign.	clinvar
BP7	Not met	Variant is a missense change (c.1081C>G, p.Arg361Gly), not a synonymous or intronic variant. BP7 applies to synonymous variants with no predicted splice impact or intronic variants outside the splice site. Not applicable to missense variants.

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