Inheritance

Autosomal dominant

Prevalence

 1:16,000 and 1:100,000.

Source: PMID: 20301642

Rapid or full curation?

ClinGen / GenCC / BabySeq / HGMD

ClinGen Hemostasis Thrombosis GCEP, Accessed 07.11.2023

Clinical Validity Scoring Notes and points

The SMAD4 gene encodes for the SMAD4 protein, belonging to the SMAD family of transcription factor proteins. SMAD4 plays a pivotal role in signal transduction of the transforming growth factor beta superfamily cytokines by mediating transcriptional activation of target genes.

Variants in SMAD4 are linked to 4 different phenotypes: juvenile polyposis with hereditary hemorrhagic telangiectasia (HHT) syndrome, Myhre syndrome, pancreatic cancer (somatic), juvenile intestinal polyposis. We curated SMAD4 for juvenile polyposis with hereditary hemorrhagic telangiectasia syndrome.

SMAD4 was first reported in relation to juvenile polyposis–HHT syndrome in 2004 (Gallione et al, PMID 15031030) in seven unrelated families or individuals displaying both juvenile polyposis and hereditary haemorrhagic telangiectasia phenotypes. Seven different variants, 4 missense, 1 stop and 2 deletions leading to frameshift, were described in the enrolled individuals. Common phenotypes were arteriovenous malformation, juvenile polyposis and telangiectasia. Epistaxis was common as well as anemia and digital clubbing.

At least 17 unique variants have been reported in humans, comprising missense, stop and frameshift variants.

Evidence supporting this gene-disease relationship includes genetic evidences (case-level data) and experimental evidences (non-human model organisms).

Summary of Case Level Data: 12 POINTS

Variants in this gene have been reported in at least 24 probands in 7 publications (PMIDs: 9582123, 15235019, 15031030, 16613914, 32944796, 30210120, 22331366) leading to a score of 12 for genetic evidence.

More evidence is available in the literature, but the maximum score for genetic evidence and/or experimental evidence has been reached. The mechanism for disease is heterozygous loss of function.

Summary of Experimental Data: 4 POINTS

This gene-disease association is supported by evidences of non-human model organisms, indeed two SMAD4 conditional knock out murine models have been described, both recapitulate most of the juvenile polyposis–HHT phenotypes including anemia and arteriovenous malformations in the brain, gastrointestinal tract, and skin (PMID 30571376) and formation of arteriovenous malformations in the neonate retina (PMID 29460088).

In summary, we found definitive association of SMAD4 with juvenile polyposis–HHT syndrome.

This classification was approved by the ClinGen Hemostasis Thrombosis Working Group on 12/16/2020 (SOP Version 8). The curation was updated on 2/22/2023 to include cases of classic Juveline polyposis with guidance from the Hereditary Cancer GCEP (SOP Version 9)

Source: ClinGen Hemostasis Thrombosis GCEP, Accessed 07.11.2023

Clinical Validity Points Total

16

Source: ClinGen Hemostasis Thrombosis GCEP, Accessed 07.11.2023

Clinical Validity Classification

Definitive

Source: ClinGen Hemostasis Thrombosis GCEP, Accessed 07.11.2023

Molecular Mechanism

Loss of function

NOTES:

Many NMD+ variants. First two pulled from ClinGen curation, but since several truncations there appeared to be NMD-, pulled additional variants from HGMD.

1. NM_005359.6(SMAD4):c.1245_1248del (p.Asp415GlufsTer20) - PMID: 30210120

   1. case report, 52yo man dx with JP-HHT.

2. NM_005359.6(SMAD4):c.692dup (p.Ser232GlnfsTer3) PMID: 9582123

   • reported in patient JP10 (table 1)

3. NM_005359.6(SMAD4):c.302G>A (p.W101*) PMID: 20101697 (table 1)

   1. Pt 4114 dx with both JP and HHT. Also has a dx of Williams syndrome.

4. NM_005359.6(SMAD4):c.692dup p.(Ser232Glnfs*3) PMID: 20101697

   1. Pt YF1, dx of both JP and HHT.

5. NM_005359.6(SMAD4):c.1102_1103del p.(Ser368Glnfs*9) 20101697

   • Pt 4269 dx with both JP and HHT

Penetrance

(list source/PMID)

Reduced, age-related

Source: https://actionability.clinicalgenome.org/ac/Pediatric/ui/stg2SummaryRpt?doc=AC066

Age of Onset

(list source/PMID)

Congenital-adulthood

Source:https://actionability.clinicalgenome.org/ac/Pediatric/ui/stg2SummaryRpt?doc=AC107 , https://actionability.clinicalgenome.org/ac/Pediatric/ui/stg2SummaryRpt?doc=AC066

Severity

Moderate

Clinical Features

• Predisposition to hamartomatous polyps in the gastrointestinal tract, specifically in the stomach, small intestine, colon, and rectum.

• Increased risk of cancer, particularly colon cancer

• Gastric polyposis, gastric cancer

• Hereditary hemorrhagic telangiectasia, characterized by arteriovenous malformations most commonly in the brain, lung, liver. Telangiectasias are small AVMs close to the surface of the skin and mucous membranes (lips, tongue, buccal, nasal, gastrointestinal mucosa, face, fingers).

• Recurrent epistaxis, anemia.

• Pulmonary arterial hypertension

Sources: https://actionability.clinicalgenome.org/ac/Pediatric/ui/stg2SummaryRpt?doc=AC107 ,

Gene SOPs & Notes

• HOMOLOGY: Please note, there is one pseudogene. Per note in https://www.ncbi.nlm.nih.gov/books/NBK535152/ it has caused false positive results in MLPA PMID: 26165824

  • Technical review and potential orthogonal confirmation may be necessary.

• Variant spectrum notes:

  • Primarily missense, nonsense, frameshift. Per GeneReviews large deletions and duplications account for 17% of SMAD4 variants.

  • Complex re-arrangements and gross insertions reported in HGMD. Tandem duplication of exon 9 reported as VUS in CLinVar (Variation ID 651595).

  • Several extension variants in HGMD, use caution when interpreting variants at the C-terminus.

Curation Summary:

The SMAD4 gene is associated with autosomal dominant juvenile polyposis - hereditary hemorrhagic telangiectasia (JP-HHT) syndrome, which is characterized by hamartomatous polyps in the gastrointestinal tract, an increased risk of cancer, arteriovenous malformations, and recurrent epistaxis (PMID: 20301642). The National Comprehensive Cancer Network (NCCN) provides guidelines for the screening and management of individuals diagnosed with JP-HHT. The SMAD4 gene is also associated with autosomal dominant Myhre syndrome, which is characterized by developmental delay and cognitive impairment, reduced growth, muscular hypertrophy, facial dysmorphism, deafness, and skeletal anomalies (PMID 22243968, 24580733).

Case ID, Curator name, Date, Jira ticket link

Andrea Oza, 07.12.2023 https://broadinstitute.atlassian.net/browse/CIT-130

Inheritance

Autosomal autosomal dominant

Prevalence

 <1 / 1 000 000

Source: ORPHA:2588

Rapid or full curation?

ClinGen / GenCC / BabySeq / HGMD

ClinGen Intellectual Disability and Autism Gene Curation Expert Panel, accessed 07.12.2023

Clinical Validity Scoring Notes and points

SMAD4 has been implicated in autosomal dominant Myhre syndrome (MONDO:0007688), generalized juvenile polyposis/juvenile polyposis coli (MONDO:0008276), and juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome (MONDO:0008278). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in molecular mechanisms and phenotypic variability among these disorders. Therefore, each of the disease entities listed above was curated separately. The current curation is for Myhre syndrome.

SMAD4 was first reported in relation to autosomal dominant Myhre syndrome in 2011 (Le Goff et al., PMID: 22158539). Individuals with Myhre syndrome present with short stature, typical facial appearance, hearing loss, laryngotracheal stenosis, skeletal abnormalities, cardiovascular abnormalities, developmental delay, mild-to-moderate intellectual disability, and autistic behavior in a minority of patients (PMIDs: 22158539, 27302097). Myhre syndrome is caused by one of four SMAD4 missense variants [c.1498A>G (p.Ile500Val); c.1499T>C (p.Ile500Thr); c.1500A>G (p.Ile500Met), and c.1486C>T (p.Arg496Cys)] (PMIDs: 22158539, 27302097, 28406602). Over 55 Myhre syndrome patients with a de novo SMAD4 pathogenic variant have been reported in the literature (PMIDs: 22158539, 26636501, 27302097, 31654632); only 9 probands were scored in this curation because the maximum score for genetic evidence has been reached. Only one inherited variant has been reported in a patient with Myhre syndrome (PMID: 31595668). SMAD4 encodes a transcription factor that regulates bone morphogenetic protein (BMP) and transforming growth factor-beta (TGFβ) signaling. The mechanism of pathogenicity is gain-of-function (PMID: 22158539). Experimental evidence supporting this gene-disease relationship includes functional assays in patient fibroblasts and cell culture models, expression studies, and model organisms (PMIDs: 16023633, 22158539, 29695415).

In summary, SMAD4 is definitively associated with autosomal dominant Myhre syndrome. This classification was approved by the ClinGen Intellectual Disability and Autism Gene Curation Expert Panel on 12/01/2021 (SOP Version 8).

Gene Clinical Validity Standard Operating Procedures (SOP) - SOP8:

Source: ClinGen Intellectual Disability and Autism Gene Curation Expert Panel, accessed 07.12.2023

Clinical Validity Points Total

14

Source: ClinGen Intellectual Disability and Autism Gene Curation Expert Panel, accessed 07.12.2023

Clinical Validity Classification

Definitive

Source: ClinGen Intellectual Disability and Autism Gene Curation Expert Panel, accessed 07.12.2023

Molecular Mechanism

Gain of function

Source: ClinGen Intellectual Disability and Autism Gene Curation Expert Panel, accessed 07.12.2023. PMID: 22158539, 24398790, 29695415

Notes:

Most studies suggest a gain-of-function effect, but more recently there has been evidence to suggest the mechanism is dominant negative.

• 22158539 - Skin fibroblasts from affected patients showed enhanced levels of SMAD4. Decreased ubiquitination of SMAD4 observed (fig 3b).

• 24398790 - In fibroblasts from affected patients, SMAD4 and phosphorylated smad2 protein levels were significantly increased compared to WT (fig 1). Cells from a Marfan syndrome patient also showed similar effect (SMAD4 and FBN1 are both involved in TGF-beta signaling pathway). Immunofluorescence showed ECM deposition defect (fig 2). Losartan treated cells had significant increase in fiber length, area, number of segments, nodes and branching points (fig 6)

• 29695415 - overexpression of SMAD 4 suppressed total dendritic length, branch numbers, and complexity. Knockdown of SMAD4 promoted dendrite development. Expressed wt and I500T in mouse hippocampal neurons and found that I500T was expressed at similar level to endogenous SMAD4 protein, the expression of this mutant enhanced dendritic growth, whereas WT SMAD4 inhibited it.

• 36194927 - dominant negative suggested. SMAD4-I500V can dimerize, but its transcriptional activity is severely compromised. HEK293T cells transfected with SMAD4 WT, I500V, OR WT/I500V. The I500V variant had reduced ability to activate TGFbeta1 and BMP4-responsive promotors (fig 1), and inhibits WT SMAD4. SMAD4 transcript levels in SMAD4-I500V- transfected cells and in WT/I500V-transfected cells were 14-fold and 21- fold increased, respectively (Fig. 4E). Co-transfection of NKX2-5 with SMAD4-I500V or with WT/I500V was able to significantly decrease the activity of NKX2-5 on both reporters (fig 5C and D).

Penetrance

(list source/PMID)

Unknown (likely high based on de novo occurrences)

Source: PMID: 28406602

Age of Onset

(list source/PMID)

Congenital

Severity

Severe

Clinical Features

Developmental disorder

Reduced growth

Generalized muscular hypertrophy

Facial dysmorphism (narrow palpebral fissures, midface hypoplasia, a small mouth with a thin upper lip, and prognathism)

Deafness

Cognitive deficits

Joint stiffness

Skeletal anomalies (thick skull bones, platispondyly, large vertebral pedicles, broad ribs, hypoplastic iliac wings, and brachydactyly)

Other: cleft lip and/or palate, congenital heart defects, stiff skin, cryptorchidism, hypertension, ocular defects

• Primarily due to de novo variants at p.Ile500 and p.Arg496

Sources: 22243968, 24580733

Gene SOPs & Notes

• HOMOLOGY: Please note, there is one pseudogene. Per note in https://www.ncbi.nlm.nih.gov/books/NBK535152/ it has caused false positive results in MLPA PMID: 26165824

  • Technical review and potential orthogonal confirmation may be necessary.

Primarily due to de novo variants at p.Ile500 and p.Arg496

Curation Summary:

SEE ABOVE (UNDER JP-HHT)

Case ID, Curator name, Date, Jira ticket link

Andrea Oza, 07.12.2023 https://broadinstitute.atlassian.net/browse/CIT-130