rs281875321

Variant names:

• chr18-51078307-T-C
• rs281875321
• NM_005359.6:c.1499T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-51078307-T-C
• chr18-51078307-T-G

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_005359.6(SMAD4):​c.1499T>C​(p.Ile500Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I500V) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SMAD4 NM_005359.6 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:10 O:2
• Conservation: PhyloP100: 7.88
• Publications: 20 publications found

Genes affected

SMAD4 (HGNC:6770): (SMAD family member 4) This gene encodes a member of the Smad family of signal transduction proteins. Smad proteins are phosphorylated and activated by transmembrane serine-threonine receptor kinases in response to transforming growth factor (TGF)-beta signaling. The product of this gene forms homomeric complexes and heteromeric complexes with other activated Smad proteins, which then accumulate in the nucleus and regulate the transcription of target genes. This protein binds to DNA and recognizes an 8-bp palindromic sequence (GTCTAGAC) called the Smad-binding element (SBE). The protein acts as a tumor suppressor and inhibits epithelial cell proliferation. It may also have an inhibitory effect on tumors by reducing angiogenesis and increasing blood vessel hyperpermeability. The encoded protein is a crucial component of the bone morphogenetic protein signaling pathway. The Smad proteins are subject to complex regulation by post-translational modifications. Mutations or deletions in this gene have been shown to result in pancreatic cancer, juvenile polyposis syndrome, and hereditary hemorrhagic telangiectasia syndrome. [provided by RefSeq, May 2022]

SMAD4 Gene-Disease associations (from GenCC):

• juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Genomics England PanelApp, G2P, PanelApp Australia
• Myhre syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, G2P, Labcorp Genetics (formerly Invitae)
• generalized juvenile polyposis/juvenile polyposis coli

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
• juvenile polyposis syndrome

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• familial thoracic aortic aneurysm and aortic dissection

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary hemorrhagic telangiectasia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• pulmonary arterial hypertension

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 16 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 14 uncertain in NM_005359.6
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr18-51078306-A-G is described in ClinVar as Pathogenic. ClinVar VariationId is 30150.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.917
• PP5: Variant 18-51078307-T-C is Pathogenic according to our data. Variant chr18-51078307-T-C is described in ClinVar as Pathogenic. ClinVar VariationId is 30149.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMAD4	NM_005359.6	c.1499T>C	p.Ile500Thr	missense_variant	Exon 12 of 12	ENST00000342988.8	NP_005350.1
SMAD4	NM_001407041.1	c.1499T>C	p.Ile500Thr	missense_variant	Exon 12 of 12		NP_001393970.1
SMAD4	NM_001407042.1	c.1499T>C	p.Ile500Thr	missense_variant	Exon 12 of 12		NP_001393971.1
SMAD4	NR_176265.1	n.2150T>C		non_coding_transcript_exon_variant	Exon 13 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMAD4	ENST00000342988.8	c.1499T>C	p.Ile500Thr	missense_variant	Exon 12 of 12	5	NM_005359.6	ENSP00000341551.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Myhre syndrome Pathogenic:6 Other:1

Jan 03, 2022

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant has been previously reported as de novo in a similarly affected individual (PMID: 22243968, PS2_S). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000030149, PMID:2215 8539, PS1_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.776, PP3_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). The variant is located in a well-established functional domain or exonic hotspot, where pathogenic variants have frequently reported (PM1_M). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000030150, PMID:22158539,22158539, PM5_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

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GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

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Jun 01, 2012

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Jul 13, 2022

Johns Hopkins Genomics, Johns Hopkins University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This SMAD4 variant (rs281875321) is absent from a large population dataset and has been reported in ClinVar. This missense change has been identified in multiple unrelated individuals with Myhre syndrome. Ile500 lies in the MAD homology 2 (MH2) domain, a region at the C-terminus of the protein, which is required for TGF-beta/BMP signal transduction. Experiments using cultured skin fibroblasts from a patient with the p.Ile500Thr substitution showed decreased levels of SMAD4 ubiquitination with increased levels of SMAD4 protein, enhanced levels of phosphorylated SMAD2/3 and SMAD1/5/8 proteins, and decreased mRNA levels of downstream TGF-beta and BMP target genes compared to controls. This variant was not detected in specimens provided by the patient's mother and father and is apparently de novo. We consider c.1499T>C to be pathogenic. -

Jun 26, 2017

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

Previously reported pathogenic variant, de novo in this case with maternity and paternity confirmed (PS2). -

May 09, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Unit U781; INSERM (Institut National de la Santé Et de la Recherche Médicale)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided Pathogenic:2 Other:1

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UniProtKB/Swiss-Prot

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

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Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jul 03, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect: significantly increased transcription activity compared to wild type (PMID: 31654632); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 22158539, 22585601, 27562837, 22243968, 27302097, 24424121, 24398790, 22683461, 24580733, 24715504, 11977156, 25252769, 30921096, 32917212, 35907855, 33057194, 35982159, 31654632, 17873119, 18823382, 15235019) -

SMAD4-related disorder Pathogenic:1

Mar 22, 2024

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The SMAD4 gene is constrained against variation (Z-score= 4.93 and pLI = 1), and missense variants are a common mechanism of disease (HGMD, ClinVar database; PMID: 28406602, 20301642). The c.1499T>C (p.Ile500Thr) variant affects a moderately conserved amino acid and in silico tools used to predict the effect of this variant on protein function yield discordant results. This is a recurrent Pathogenic variant that has been previously reported as a de novo heterozygous change in patients with Myhre syndrome (PMID: 37529930, 26420300, 22243968, 22158539, 27302097). The c.1499T>C (p.Ile500Thr) variant is located in the MAD homology 2 domain, which is required for signal transduction and is a known hotspot domain for pathogenic variations associated with Myhre syndrome (HGMD, PMID: 24580733, 38066625, 36194927). Different amino acid changes at the same residue (p.Ile500Val and p.Ile500Met) have been previously reported in individuals with Myhre syndrome (PMID: 24580733). Functional studies demonstrated that the c.1499T>C (p.Ile500Thr) variant results in defective transcriptional regulation related to increased SMAD4 protein expression, decreased levels of SMAD4 ubiquitination, increased levels of SMAD phosphorylation, and decreased mRNA levels of TGF-beta and BMP target genes in comparison to controls (PMID: 22158539). The c.1499T>C (p.Ile500Thr) variant is absent from the gnomAD v4 population database and thus is presumed to be rare. Based on the available evidence, c.1499T>C (p.Ile500Thr) is classified as Pathogenic. -

Juvenile polyposis syndrome Pathogenic:1

Mar 25, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been observed in individual(s) with Myhre syndrome (PMID: 22158539, 27302097, 30921096, 24424121, 22243968). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 30149). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Ile500 amino acid residue in SMAD4. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 22158539, 22243968, 22585601, 24398790, 26636501, 27302097, 24398790). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this variant affects SMAD4 protein function (PMID: 31654632, 22158539). This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with threonine at codon 500 of the SMAD4 protein (p.Ile500Thr). The isoleucine residue is highly conserved and there is a moderate physicochemical difference between isoleucine and threonine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	27
DANN	Benign	0.92
DEOGEN2	Pathogenic	0.96	D;D;D
Eigen	Uncertain	0.39
Eigen_PC	Uncertain	0.45
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.90	.;D;D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.92	D;D;D
MetaSVM	Uncertain	0.78	D
MutationAssessor	Benign	1.2	L;L;.
PhyloP100		7.9
PrimateAI	Pathogenic	0.94	D
PROVEAN	Uncertain	-3.9	D;D;.
REVEL	Pathogenic	0.78
Sift	Benign	0.33	T;T;.
Sift4G	Benign	1.0	T;T;T
Polyphen		1.0	D;D;.
Vest4		0.93
MutPred		0.55		Loss of stability (P = 0.0363);Loss of stability (P = 0.0363);.;
MVP		0.96
MPC		3.2
ClinPred		0.98	D
GERP RS		4.9
Varity_R		0.68
gMVP		0.94
Mutation Taster		=12/88	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs281875321; hg19: chr18-48604677;