Variant classification summary

NM_005359.5:c.1081C>A

SMAD4 · NP_005350.1:p.(Arg361Ser) · NM_005359.5

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

Gene: SMAD4 Transcript: NM_005359.5

Final call

Likely Pathogenic

PM1 moderate PM2 supporting PM5 moderate PP2 supporting PP3 supporting PP5 supporting

Variant details

Gene

SMAD4

Transcript

NM_005359.5

Protein

NP_005350.1:p.(Arg361Ser)

gnomAD AF

ClinVar

Likely pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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).

2

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).

3

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).

4

Multiple in silico tools predict a deleterious effect: REVEL score 0.912 and BayesDel score 0.534, meeting PP3 (supporting).

5

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).

6

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.

7

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).

8

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).

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of 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	PVS1 is not applicable to missense variants. This variant (c.1081C>A, p.Arg361Ser) is a missense substitution in exon 9 of SMAD4 and does not fall into the null-variant categories (nonsense, frameshift, or canonical ±1,2 splice consensus) required for PVS1 under the ClinGen SVI PVS1 framework (PMC6185798).	pvs1_generic_framework
PS1	Not met	PS1 requires the same amino acid change (p.Arg361Ser) to have been previously established as pathogenic. No pathogenic or likely pathogenic variant with p.Arg361Ser has been identified in ClinVar or the reviewed literature. Different pathogenic missense changes at the same residue (p.Arg361Cys, p.Arg361His, p.Arg361Leu) do not satisfy PS1, though they are captured under PM5.	clinvar PMID:11583957 PMID:16613914 PMID:17873119 PMID:20101697
PS2	Not assessed	No de novo data specific to NM_005359.5:c.1081C>A (p.Arg361Ser) were identified in the reviewed literature or ClinVar submissions. De novo status cannot be assessed without parental testing data for this exact variant.
PS3	Not assessed	No functional studies specific to p.Arg361Ser were identified. The structural and functional characterization of SMAD4 missense variants at codon 361 (PMID:9214508) evaluated p.Arg361Cys but not p.Arg361Ser. Although the residue is critical for SMAD4 MH2 domain hetero- and homo-oligomerization, variant-specific functional data for p.Arg361Ser are absent.	PMID:9214508 PMID:11583957
PS4	Not assessed	The variant is absent from population databases and has a single ClinVar submission as Likely pathogenic. No formal case-control study comparing affected vs. unaffected individuals for this specific variant is available. Prevalence data are insufficient to apply PS4.	gnomad_v2 gnomad_v4 clinvar
PS5	N/A	PS5 requires the same nucleotide change to have been previously established as pathogenic. No independently established pathogenic variant at c.1081C>A exists; the single ClinVar submission for this variant (Likely pathogenic, single submitter) does not constitute independent establishment.	clinvar
PM1	Met	c.1081C>A (p.Arg361Ser) is located in the MH2 domain of SMAD4 (codons 323-552), a well-established mutational hotspot. Codon 361 harbors multiple independently reported pathogenic missense mutations (p.Arg361Cys, p.Arg361His, p.Arg361Leu) in patients with juvenile polyposis syndrome (JPS) and JP-HHT syndrome. Additionally, this residue lies in a statistically significant somatic hotspot in COSMIC (n=16).	PMID:9811934 PMID:11583957 PMID:16613914 PMID:17873119 PMID:20101697 oncokb
PM2	Met	NM_005359.5:c.1081C>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). Under generic ACMG/AMP 2015 criteria, absence from large population databases at an allele frequency below 0.1% supports PM2 at supporting strength.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Met	c.1081C>A produces a novel missense change p.Arg361Ser at codon 361, where multiple different pathogenic missense variants are established: p.Arg361Cys (c.1081C>T) is reported in multiple JPS and HHT families (PMID:9811934, PMID:11583957, PMID:16613914, PMID:17873119, PMID:20101697); p.Arg361His (c.1082G>A) is reported as a de novo JPS mutation (PMID:17873119); and p.Arg361Leu (c.1082G>T) is reported in a JP-HHT patient (PMID:20101697).	PMID:9811934 PMID:11583957 PMID:16613914 PMID:17873119 PMID:20101697
PM6	Not assessed	No de novo confirmation for this specific variant was identified. PM6 requires confirmed de novo occurrence with parental testing, which is not available for NM_005359.5:c.1081C>A.
PP1	Not assessed	No co-segregation data are available for NM_005359.5:c.1081C>A. None of the reviewed publications reported this specific variant in a family context suitable for segregation analysis.
PP2	Met	SMAD4 is a gene in which missense variants are a well-established mechanism of disease. Multiple pathogenic missense mutations are documented across the gene, particularly in the MH2 domain, in juvenile polyposis syndrome (JPS), hereditary hemorrhagic telangiectasia (HHT), and JP-HHT syndrome. Benign missense variation in SMAD4 is rare, consistent with a high constraint against missense changes.	PMID:20101697 PMID:17873119 PMID:11583957 PMID:9811934
PP3	Met	Multiple in silico prediction tools support a deleterious effect: REVEL score 0.912 (threshold >0.7), BayesDel score 0.534 (threshold >0.5). SpliceAI predicts no significant splicing impact (max delta = 0.14). The combined in silico evidence supports a damaging effect on protein function.	revel bayesdel spliceai
PP4	Not assessed	No proband phenotype data specific to this variant are available for evaluation. PP4 requires the variant to be identified in a patient with a phenotype highly specific for the gene/disease, which cannot be assessed without clinical records.
PP5	Met	This variant has been reported as Likely pathogenic by a clinical diagnostic laboratory (Labcorp Genetics/Invitae; SCV002282679) in ClinVar (VariationID 24822) with criteria provided. Under generic ACMG/AMP 2015, a single reputable clinical laboratory classification of Likely pathogenic with supporting criteria contributes PP5 at supporting strength.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. BA1 requires an allele frequency >1% in any large population database, which is not satisfied.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from gnomAD. BS1 requires an allele frequency >0.3% in population databases, which is not satisfied.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not assessed	No data on observation of this variant in healthy adult individuals are available. BS2 requires documentation that the variant has been observed in a healthy adult without the associated disease phenotype.
BS3	Not met	No functional studies demonstrate a neutral or benign effect of p.Arg361Ser. Available in silico evidence (REVEL 0.912, BayesDel 0.534) strongly predicts a damaging effect. The well-characterized functional impact of different missense changes at the same residue (p.Arg361Cys abolishes SMAD4 oligomerization per PMID:9214508) supports a deleterious effect rather than a benign one.	PMID:9214508 revel bayesdel
BS4	Not assessed	No segregation data are available to evaluate lack of co-segregation with disease. BS4 cannot be assessed without family studies for this variant.
BP1	N/A	BP1 applies to missense variants in genes where only truncating variants cause disease. SMAD4 has numerous well-documented pathogenic missense mutations (including at codon 361) that cause JPS, HHT, and JP-HHT syndrome. Therefore BP1 is not applicable.	PMID:11583957 PMID:17873119 PMID:20101697
BP2	N/A	BP2 applies to observation of the variant in trans with a known pathogenic variant for a fully penetrant dominant disorder. No such data are available for this variant; however, SMAD4-related disorders are autosomal dominant with haploinsufficiency as the mechanism, so observation in trans is not expected.
BP4	Not met	BP4 requires multiple in silico tools to predict no impact on the gene product. In contrast, REVEL (0.912) and BayesDel (0.534) both predict a deleterious effect. SpliceAI shows no significant splicing impact (max delta 0.14), but this alone is insufficient to meet BP4 when protein-level predictors are strongly damaging.	revel bayesdel spliceai
BP5	Not assessed	No alternative molecular basis for disease has been identified in cases carrying this variant. BP5 is not applicable without proband-level data showing an alternative cause.
BP6	Not met	BP6 requires a reputable source to classify the variant as benign. ClinVar classifies this variant as Likely pathogenic (VariationID 24822). No benign classification exists from any source.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. NM_005359.5:c.1081C>A is a missense variant (p.Arg361Ser), not synonymous.

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