rs281875322

Positions:

• chr18-51078306-A-G
• chr18-51078306-A-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PM5 PP2 PP5_Very_Strong

The NM_005359.6(SMAD4):​c.1498A>G​(p.Ile500Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: SMAD4 NM_005359.6 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:38 O:2
• Conservation: PhyloP100: 9.17

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 15 ACMG points.

• PM1: In a strand (size 6) in uniprot entity SMAD4_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) 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 chr18-51078308-A-G is described in Lovd as [Pathogenic].
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SMAD4. . Gene score misZ 4.1308 (greater than the threshold 3.09). Trascript score misZ 4.9346 (greater than threshold 3.09). GenCC has associacion of gene with familial thoracic aortic aneurysm and aortic dissection, generalized juvenile polyposis/juvenile polyposis coli, hereditary hemorrhagic telangiectasia, Myhre syndrome, pulmonary arterial hypertension, juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, juvenile polyposis syndrome.
• PP5: Variant 18-51078306-A-G is Pathogenic according to our data. 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. Variant chr18-51078306-A-G is described in Lovd as [Pathogenic]. Variant chr18-51078306-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMAD4	NM_005359.6	c.1498A>G	p.Ile500Val	missense_variant	12/12	ENST00000342988.8	NP_005350.1
SMAD4	NM_001407041.1	c.1498A>G	p.Ile500Val	missense_variant	12/12		NP_001393970.1
SMAD4	NM_001407042.1	c.1498A>G	p.Ile500Val	missense_variant	12/12		NP_001393971.1
SMAD4	NR_176265.1	n.2149A>G		non_coding_transcript_exon_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAD4	ENST00000342988.8	c.1498A>G	p.Ile500Val	missense_variant	12/12	5	NM_005359.6	ENSP00000341551	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251462 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135902

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461882 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727242

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:38 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Myhre syndrome Pathogenic:18 Other:1

not provided, no classification provided	literature only	GeneReviews	-	- -
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	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	Dec 19, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Dec 18, 2017	- -
Pathogenic, criteria provided, single submitter	research	Duke University Health System Sequencing Clinic, Duke University Health System	Apr 20, 2023	- -
Pathogenic, no assertion criteria provided	clinical testing	Molecular Diagnosis Center for Deafness	Nov 02, 2021	- -
Pathogenic, no assertion criteria provided	research	Shieh Lab, University of California, San Francisco	Oct 19, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Nov 08, 2018	- -
Pathogenic, no assertion criteria provided	clinical testing	Institute of Human Genetics, Heidelberg University	Oct 20, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	Sep 05, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Pediatric Genetics Clinic, Sheba Medical Center	May 13, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Oct 02, 2021	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000030150.18, PS1). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.00000397, PM2). A different missense change at the same codon (p.Ile500Thr) has been reported as pathogenic (ClinVar ID:VCV000030149.3, PM5). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.71, PP3). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Apr 13, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine	Mar 04, 2021	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Sep 21, 2020	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Pathogenic, criteria provided, single submitter	clinical testing	Provincial Medical Genetics Program of British Columbia, University of British Columbia	Jan 01, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Aug 23, 2022	PM1, PM2, PM5, PP3, PP5 -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jun 24, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with juvenile intestinal polyposis or juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome (MIM#174900, MIM#175050), and Myhre syndrome (MIM#139210), respectively (OMIM, PMID: 31837202). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from isoleucine to valine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and high conservation. (I) 0600 - Variant is located in the annotated MH2 domain (DECIPHER). (I) 0703 - Another missense variant comparable to the one identified in this case has moderate previous evidence for pathogenicity. p.(Ile500Thr) has been classified as pathogenic by several clinical laboratories in ClinVar. (SP) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by multiple clinical laboratories in ClinVar and has been observed as de novo in several individuals with syndromic developmental delay or intellectual disability (DECIPHER). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

not provided Pathogenic:11 Other:1

not provided, no classification provided	literature only	UniProtKB/Swiss-Prot	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes	Jul 31, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Nov 26, 2022	The SMAD4 c.1498A>G (p.Ile500Val) missense variant results in the substitution of isoleucine at amino acid position 500 with valine. This variant is the most commonly reported variant in Myhre syndrome and has been described in at least 34 affected individuals, in many of whom it occurred de novo (PMID: 27302097; PMID: 36194927). The c.1498A>G variant is reported in the Genome Aggregation Database in one allele at a frequency of 0.000009 in the European (non-Finnish) population (version 2.1.1). Two other missense changes affecting the same position, p.Ile500Thr and p.Ile500Met, have also been reported in individuals with Myhre syndrome (PMID: 27302097). The valine and threonine changes have been shown to disrupt TGF-β and BMP signaling in HEK293T cells and patient fibroblasts, and the p.Ile500Val variant has been specifically shown to have a dominant-negative effect on wild-type SMAD4 (PMID: 22158539; PMID 36194927). Based on the available evidence, the c.1498A>G (p.Ile500Val) variant is classified as pathogenic for Myhre syndrome. -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	SMAD4: PS2:Very Strong, PM1, PM2, PM5, PP2, PP3, PS3:Supporting, PS4:Supporting -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Jun 27, 2022	PM1, PS3, PP3, PM5, PM2_SUP -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 16, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 01, 2022	Published functional studies demonstrate a damaging effect as p.(I500V) resulted in dysregulation of both matrix metalloproteinases and related inhibitors (Piccolo et al., 2014); In silico analysis supports that this missense variant does not alter protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26633542, 34620752, 34556655, 34849273, 22243968, 22585601, 22158539, 27302097, 26636501, 27562837, 25533962, 25363768, 28991257, 28191890, 30921096, 29230941, 28562390, 28867141, 31654632, 32021609, 32175297, 31618753, 31447099, 28714951, 32371413, 32368696, 34015905, 30787465, 31785789, 17873119, 18823382, 15235019, 24398790) -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Mar 26, 2024	- -

Juvenile polyposis syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 01, 2023	This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 500 of the SMAD4 protein (p.Ile500Val). This variant is present in population databases (rs281875322, gnomAD 0.0009%). This missense change has been observed in individual(s) with Myhre syndrome (PMID: 22158539, 22243968, 22585601, 24398790, 26636501, 27302097). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 30150). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SMAD4 protein function. Experimental studies have shown that this missense change affects SMAD4 function (PMID: 24398790). 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, 22683461). 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. -
Pathogenic, criteria provided, single submitter	clinical testing	DASA	Jan 05, 2022	The c.1498A>G;p.(Ile500Val) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 30150; OMIM: 600993.0016; PMID: 28406602; 22158539; 22243968; 22585601; 24398790; 26636501; 27302097) - PS4. Well-established in vitro or in vivo functional studies support a damaging effect on the gene or gene product (PMID 24398790) - PS3. This variant is not present in population databases (rs281875322, gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. Pathogenic missense variant in this residue have been reported (ClinVar ID: 30149) - PM5. Missense variant in SMAD4 that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease - PP2. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic. -

Neurodevelopmental delay Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genomic Medicine Lab, University of California San Francisco

Apr 16, 2020

- -

SMAD4-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 20, 2024

The SMAD4 c.1498A>G variant is predicted to result in the amino acid substitution p.Ile500Val. This variant has been reported to be a recurrent cause of Myhre syndrome and has been reported de novo in multiple individuals (see, for example, Le Goff et al. 2011. PubMed ID: 22158539; Alagia et al. 2018. PubMed ID: 29230941; Yu et al. 2019. PubMed ID: 30921096; Li et al. 2020. PubMed ID: 31654632). In vitro experimental studies suggest this variant affects protein function (Piccolo et al. 2014. PubMed ID: 24398790). Alternative nucleotide changes affecting the same amino acid (p.Ile500Thr, p.Ile500Met) have also been reported in patients with Myhre syndrome (Le Goff et al. 2011. PubMed ID: 22158539).This variant is reported in 0.00088% of alleles in individuals of European (non-Finnish) descent in gnomAD. It is interpreted in ClinVar as pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/30150/). This variant is interpreted as pathogenic. -

Hereditary cancer-predisposing syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 09, 2021

The c.1498A>G (p.I500V) alteration is located in exon 12 (coding exon 11) of the SMAD4 gene. This alteration results from an A to G substitution at nucleotide position 1498, causing the isoleucine (I) at amino acid position 500 to be replaced by a valine (V). Based on data from the Genome Aggregation Database (gnomAD), the SMAD4 c.1498A>G alteration was observed in <0.01% (1/251462) of total alleles studied. This alteration has been previously reported as de novo in multiple unrelated patients with Myhre syndrome and affects a known mutational hotspot (Le Goff, 2011; Caputo, 2012; Lin 2016; Alagia, 2018; Yu, 2019; Varenyiova, 2020). This amino acid position is highly conserved in available vertebrate species. Functional analysis demonstrated that the p.I500V alteration interferes with ubiquitination and degradation of SMAD4 resulting in accumulation of protein and induction of the TGFbeta pathway (Le Goff, 2011; Caputo, 2012; Piccolo, 2014). The in silico prediction for the p.I500V alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -

Carcinoma of pancreas;C0796081:Myhre syndrome;C1832942:Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome;C1868081:Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Myhre syndrome;C1832942:Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome;C1868081:Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital

Mar 11, 2019

[ACMG/AMP: PS2, PS3, PM1, PM2, PM5, PP2, PP3, PP5] This alteration is de novo in origin as it was not detected in the submitted parental specimens (identity confirmed) [PS2], is supported by well-established in vitro or in vivo functional studies to have a damaging effect on protein function or splicing [PS3], is located in a mutational hotspot and/or critical and well-established functional domain [PM1], is absent from or rarely observed in large-scale population databases [PM2], is a novel missense change at an amino residue where a different missense change has been deemed to be pathogenic [PM5], is a missense variant in a gene in which missense variants are a common mechanism of disease [PP2], is predicted to be damaging by multiple functional prediction tools [PP3], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5]. -

Intellectual disability Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Diagnostic Laboratory, Strasbourg University Hospital

Sep 10, 2020

- -

Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Apr 27, 2018

SMAD4, c.1498A>G, p.Ile500Val The c.1498A>G (p. Ile500Val) variant in the SMAD4 gene has been reported in multiple individuals with MYRHE syndrome (PMID 22158539, 22243968, 22585601, 24398790, 26636501, 27302097). This variant is observed with an ultra-low minor allele frequency in the gnomAD database (1/246232). This variant is on a known mutation hot spot with another pathogenic variant p.Ile500Thr. Functional studies on this variant suggested increased SMAD4 protein levels and increased TGF-beta signaling (PMID 24398790). Therefore, the c.1498A>G (p. Ile500Val) variant in the SMAD4 gene is classified as pathogenic -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.62
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.28
CADD	Uncertain	26
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.82	D;D;D
Eigen	Pathogenic	0.80
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	.;D;D
M_CAP	Pathogenic	0.30	D
MetaRNN	Uncertain	0.69	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Benign	1.9	L;L;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-0.84	N;N;.
REVEL	Pathogenic	0.71
Sift	Benign	0.041	D;D;.
Sift4G	Benign	0.59	T;T;T
Polyphen		0.99	D;D;.
Vest4		0.72
MutPred		0.52		Gain of catalytic residue at I500 (P = 0.0315);Gain of catalytic residue at I500 (P = 0.0315);.;
MVP		0.94
MPC		2.2
ClinPred		0.71	D
GERP RS		6.1
Varity_R		0.49
gMVP		0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs281875322; hg19: chr18-48604676;