18-51078306-A-G
Variant summary
Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PM1PM2PM5PP5_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. I500T) has been classified as Pathogenic.
Frequency
Consequence
NM_005359.6 missense
Scores
Clinical Significance
Conservation
Publications
- juvenile polyposis/hereditary hemorrhagic telangiectasia syndromeInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Genomics England PanelApp, G2P, PanelApp Australia
- Myhre syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, G2P, Labcorp Genetics (formerly Invitae)
- generalized juvenile polyposis/juvenile polyposis coliInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
- juvenile polyposis syndromeInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- familial thoracic aortic aneurysm and aortic dissectionInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hereditary hemorrhagic telangiectasiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- pulmonary arterial hypertensionInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Our verdict: Pathogenic. The variant received 14 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005359.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SMAD4 | NM_005359.6 | MANE Select | c.1498A>G | p.Ile500Val | missense | Exon 12 of 12 | NP_005350.1 | ||
| SMAD4 | NM_001407041.1 | c.1498A>G | p.Ile500Val | missense | Exon 12 of 12 | NP_001393970.1 | |||
| SMAD4 | NM_001407042.1 | c.1498A>G | p.Ile500Val | missense | Exon 12 of 12 | NP_001393971.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SMAD4 | ENST00000342988.8 | TSL:5 MANE Select | c.1498A>G | p.Ile500Val | missense | Exon 12 of 12 | ENSP00000341551.3 | ||
| SMAD4 | ENST00000591126.5 | TSL:1 | n.3499A>G | non_coding_transcript_exon | Exon 8 of 8 | ||||
| SMAD4 | ENST00000714264.1 | c.1579A>G | p.Ile527Val | missense | Exon 12 of 12 | ENSP00000519545.1 |
Frequencies
GnomAD3 genomes
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251462 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727242 show subpopulations
GnomAD4 genome
ClinVar
Submissions by phenotype
Myhre syndrome Pathogenic:21Other:1
Variant: c.1498A>G (p.Ile500Val) in exon 12 of the SMAD4 gene. Zygosity and phenotype: Identified in the heterozygous state in affected individual; phenotype consistent with Myhre Syndrome. Protein effect: Missense substitution within the MAD homology domain 2, a well-established functional region where pathogenic variants are frequently reported. Functional studies show compromised activation of the TGF-β pathway, consistent with a dominant-negative mechanism associated with Myhre syndrome (PMID: 36194927). Conservation and in silico evidence: Residue highly conserved across species; pathogenicity predictors indicate deleterious effect on protein function (REVEL score: 0.71). SMAD4 has low rate for benign missense variants (z-score: 4.94). Population data: Low allele frequency in population databases (gnomAD); Residue evidence: Another pathogenic missense change at the same residue has been reported (Accession: VCV000030149.19). ClinVar: Reported in multiple individuals as Pathogenic (ID:30150) Segregation/compound data: Segregation analyses, with and without confirmation of paternity, indicate a de novo occurrence (PMID: 22243968, 29230941, 31654632). ACMG/AMP criteria applied: PS2, PS3_Supporting, PS4_Moderate, PM1, PM2_Supporting, PM5, PP2, PP3, following ClinGen SVI recommendations.
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
The variant is observed at an extremely low frequency in the gnomAD v4.0.0 dataset (total allele frequency: <0.001%). Predicted Consequence/Location: The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PMID: 22158539). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.71 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.77 (>=0.6, sensitivity 0.72 and precision 0.9)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000030150 /PMID: 22158539).The variant has been previously reported as de novo in a similarly affected individual (PMID: 25533962).The variant has been previously reported as assumed (i.e. paternity and maternity not confirmed) de novo in at least one similarly affected unrelated individual (3billion dataset).Different missense changes at the same codon (p.Ile500Met, p.Ile500Thr) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000030149, VCV000030151 /PMID: 22158539 /3billion dataset). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
PM1, PM2, PM5, PP3, PP5
Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.;Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.;The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.;Assumed de novo, but without confirmation of paternity and maternity.
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
This sequence variant is a single nucleotide substitution (A>G) at coding position 1498 of the SMAD4 gene that results in a isoleucine to valine amino acid change at residue 500 of the SMAD4 protein. The Ile500 residue falls in the Mad Homology 2 domain which plays a critical role in the maintence of the extracellular matrix (PMID:24398790). This is a well-studied, previously reported variant (ClinVar, Gene Reviews, PMID: 28406602) that has been observed in individuals affected by Myhre syndrome (PMID:24398790, 27302097, 35907855, 22243968, 28406602). This variant is present in 1 of 251,462 alleles (0.0004%) in the gnomAD population database. Multiple bioinformatic tools predict that this isoleucine to valine amino acid change would be damaging, and the isoleucine residue is highly conserved across the vertebrate species examined. Cultured cells containing this variant had an increased production of SMAD4, an altered pattern of gene expression related to the maintence of the extracelluar matrix, and a disrupted extracellular matrix (PMID: 24398790). Given this information, we consider this a pathogenic variant. ACMG Criteria: PM2, PP2, PS3, PS4
not provided Pathogenic:12Other:1
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.
SMAD4: PS2:Very Strong, PM1, PM2, PM5, PP2, PP3, PS3:Supporting, PS4:Supporting
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)
PM1, PS3, PP3, PM5, PM2_SUP
SMAD4-related disorder Pathogenic:2
PS2, PS3, PM1, PM2, PM5
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.
Juvenile polyposis syndrome Pathogenic:2
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.
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). Invitae Evidence 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 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.
Neurodevelopmental delay Pathogenic:1
Hereditary cancer-predisposing syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1
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). for Myhre syndrome; however, its clinical significance for juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome is uncertain. 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). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
Intellectual disability Pathogenic:1
Myhre syndrome;C1832942:Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome;C1868081:Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1
[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].
Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome Pathogenic:1
Familial aortopathy Pathogenic:1
Variant summary: SMAD4 c.1498A>G (p.Ile500Val) results in a conservative amino acid change in the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change. The variant allele was found at a frequency of 4e-06 in 251462 control chromosomes (gnomAD). c.1498A>G has been observed in multiple individuals affected with Myhre syndrome (e.g, Michot_2014). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 24424121). ClinVar contains an entry for this variant (Variation ID: 30150). Based on the evidence outlined above, the variant was classified as pathogenic.
Familial renal glucosuria Pathogenic:1
This SMAD4 variant (rs281875322) is rare (<0.1%) in a large population dataset (gnomADv2.1.1: 1/251462 total alleles; 0.0004%; no homozygotes) and has been reported in ClinVar. This variant is the most commonly reported variant in Myhre syndrome and has been described in multiple unrelated individuals, typically as a de novo change. Experiments using p.Ile500Val patient fibroblasts have shown a disruption of TGF-B and BMP signaling. Two other missense changes affecting the same position, p.Ile500Thr and p.Ile500Met, have also been reported in individuals with Myhre syndrome. We consider c.1498A>G to be pathogenic for autosomal dominant Myhre syndrome.
Carcinoma of pancreas;C0796081:Myhre syndrome;C1832942:Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome;C1868081:Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1
Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at