rs281875321

chr18-51078307-T-Cchr18-51078307-T-G

Variant summary

Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1 PM2 PM5 PP2 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. I500M) 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:9 O:2
• Conservation: PhyloP100: 7.88

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]

ACMG classification

Verdict is Pathogenic. Variant got 17 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, 8 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 id is 30150.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant where missense usually causes diseases, SMAD4
• 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 id is 30149.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-51078307-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMAD4	NM_005359.6	c.1499T>C	p.Ile500Thr	missense_variant	12/12	ENST00000342988.8
SMAD4	NM_001407041.1	c.1499T>C	p.Ile500Thr	missense_variant	12/12
SMAD4	NM_001407042.1	c.1499T>C	p.Ile500Thr	missense_variant	12/12
SMAD4	NR_176265.1	n.2150T>C		non_coding_transcript_exon_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMAD4	ENST00000342988.8	c.1499T>C	p.Ile500Thr	missense_variant	12/12	5	NM_005359.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Myhre syndrome Pathogenic:6 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Jul 13, 2022	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. -
Pathogenic, criteria provided, single submitter	research	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jun 26, 2017	Previously reported pathogenic variant, de novo in this case with maternity and paternity confirmed (PS2). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 2012	- -
Pathogenic, no assertion criteria provided	literature only	Unit U781; INSERM (Institut National de la Santé Et de la Recherche Médicale)	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	May 09, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	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. -
not provided, no classification provided	literature only	GeneReviews	-	- -

not provided Pathogenic:2 Other:1

not provided, no classification provided	literature only	UniProtKB/Swiss-Prot	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 20, 2021	Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 22158539, 22585601, 27562837, 22243968, 27302097, 24424121, 24398790, 22683461, 24580733, 24715504, 11977156, 25252769, 30921096, 31654632, 32917212) -
Pathogenic, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -

Juvenile polyposis syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Mar 25, 2021

Experimental studies have shown that this variant affects SMAD4 protein function (PMID: 31654632, 22158539). 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). 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. 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. For these reasons, this variant has been classified as Pathogenic. -

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
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.92	D;D;D
MetaSVM	Uncertain	0.78	D
MutationAssessor	Benign	1.2	L;L;.
MutationTaster	Benign	1.0	D;D;D
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

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

Publications

LitVar

Other links and lift over

dbSNP: rs281875321; hg19: chr18-48604677;