rs80338965
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_005359.6(SMAD4):c.1245_1248delCAGA(p.Asp415GlufsTer20) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,458,726 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005359.6 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SMAD4 | NM_005359.6 | c.1245_1248delCAGA | p.Asp415GlufsTer20 | frameshift_variant | Exon 10 of 12 | ENST00000342988.8 | NP_005350.1 | |
| SMAD4 | NM_001407041.1 | c.1245_1248delCAGA | p.Asp415GlufsTer20 | frameshift_variant | Exon 10 of 12 | NP_001393970.1 | ||
| SMAD4 | NM_001407042.1 | c.1245_1248delCAGA | p.Asp415GlufsTer20 | frameshift_variant | Exon 10 of 12 | NP_001393971.1 | ||
| SMAD4 | NR_176265.1 | n.1783_1786delCAGA | non_coding_transcript_exon_variant | Exon 10 of 13 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458726Hom.: 0 AF XY: 0.00000276 AC XY: 2AN XY: 725948
GnomAD4 genome
ClinVar
Submissions by phenotype
not provided Pathogenic:4
This variant alters the translational reading frame of the SMAD4 mRNA and causes the premature termination of SMAD4 protein synthesis. In the published literature, this variant has been reported in multiple individuals with juvenile polyposis syndrome (JPS) (PMID: 33097490 (2021), 27375208 (2016), 23239472 (2013), 18355998 (2008), 17873119 (2007), 10398437 (1999), 9582123 (1998)). In a functional study, the variant reduced downstream bone morphogenic protein signaling in vitro (PMID: 22316667 (2012)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate a damaging effect: decreased BMP-mediated transcriptional activity (Carr et al., 2012); Observed in individuals with a personal or family history consistent with pathogenic variants in this gene referred for testing at GeneDx and in the published literature (Aretz et al.,2007; Calva-Cerqueira et al., 2009; Gallione et al., 2010; Ngeow et al., 2013; Teekakirikul et al., 2013; Bruceta et al., 2018; Inoguchi et al., 2019); Segregates with disease in many affected individuals from several families referred for genetic testing at GeneDx and in published literature (Howe et al., 1998; Piepoli et al., 2012; Burmester et al., 2016); Not observed at significant frequency in large population cohorts (gnomAD); Also known as 1244_1247delACAG, 1372_1375del4, and 1242_45delAGAC; This variant is associated with the following publications: (PMID: 15235019, 24506336, 16152648, 26681312, 20101697, 18355998, 25931195, 23239472, 9582123, 22748914, 23399955, 17873119, 18823382, 27375208, 28526081, 28944238, 28152038, 30210120, 29634562, 31447099, 33097490, 30787465, 27535533, 22316667, 26171675) -
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Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:3Other:1
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The p.Asp415GlufsX20 variant in SMAD4 has been reported in >20 probands (2 de no vo occurrences) with juvenile polyposis syndrome (JPS) and segregated with disea se in >20 relatives of multiple families (Howe 1998, Handra-Luca 2005, Calva-Cer queira 2009, Piepoli 2012, Ngeow 2013, Teekakirikul 2013, AlBalwi 2015, Susswein 2015, Burmester 2016, DeRycke 2017). This variant was absent from large populat ion databases but has been reported in ClinVar (Variation ID: 142253). This vari ant is predicted to cause a frameshift, which alters the protein?s amino acid se quence beginning at position 415 and leads to a premature termination codon 20 a mino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Heterozygous loss of function of the SMAD4 gene is an establi shed disease mechanism in JPS. In addition, in vitro functional studies provide some evidence that the p.Asp415GlufsX20 variant may impact protein function (Car r 2012). In summary, this variant meets criteria to be classified as pathogenic for JPS in an autosomal dominant manner based upon prevalence in probands, segre gation studies, absence from controls, functional evidence, and the predicted im pact on protein. ACMG/AMP Criteria applied: PVS1, PS4, PM6_Strong, PP1_Strong, P M2. -
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Variant summary: SMAD4 c.1245_1248delCAGA (p.Asp415GlufsX20) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251950 control chromosomes (gnomAD and publication). c.1245_1248delCAGA has been reported in the literature in multiple individuals affected with Juvenile Polyposis Syndrome and was also shown to segregate with the disease (Carr_2012, Howe_1998). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function demonstrated the variant leads to decreased bone morphogenetic protein signaling (Carr_2012). Six ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome Pathogenic:3
The variant NM_005359.6:c.1245_1248del (chr18:51067120) in SMAD4 was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). This variant has been reported in ClinVar previously as pathogenic. Based on ACMG criteria (PVS1, PM2) this variant classifies as likely pathogenic. -
Variant confirmed as disease-causing by referring clinical team -
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -
Juvenile polyposis syndrome Pathogenic:2
This sequence change creates a premature translational stop signal (p.Asp415Glufs*20) in the SMAD4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SMAD4 are known to be pathogenic (PMID: 16152648, 16436638, 22810475). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with juvenile polyposis syndrome (JPS) (PMID: 9582123, 17873119, 18355998, 23239472, 23399955, 27375208). It has also been observed to segregate with disease in related individuals. This variant is also known as 1244_7delACAG and as a 4-bp deletion between nucleotides 1372 and 1375. ClinVar contains an entry for this variant (Variation ID: 142253). For these reasons, this variant has been classified as Pathogenic. -
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SMAD4-related disorder Pathogenic:1
The SMAD4 c.1245_1248delCAGA variant is predicted to result in a frameshift and premature protein termination (p.Asp415Glufs*20). This variant has been reported in individuals with juvenile polyposis syndrome and shown to segregate with disease in families (see, for example, Howe et al. 1998. PubMed ID: 9582123; Calva-Cerqueira et al. 2009. PubMed ID: 18823382; Supplementary Table 2, Ngeow et al. 2013. PubMed ID: 23399955). It has also been reported in an individual with juvenile polyposis-hereditary hemorrhagic telangiectasia syndrome (Teekakirikul et al. 2013. PubMed ID: 23239472). In vitro functional studies suggest this variant impacts protein function (described as Del AGAC 1244-47 D415EfsX20 in Carr et al. 2012. PubMed ID: 22316667). This variant has not been reported in a large population database, indicating it is rare. Frameshift variants in SMAD4 are expected to be pathogenic. This variant is interpreted as pathogenic. -
Carcinoma of colon Pathogenic:1
The SMAD4 p.Asp415Glufs*20 variant was identified in 21 of 1596 proband chromosomes (frequency: 0.01) from individuals or families with juvenile and moderate-load polyposis and was not identified in 484 control chromosomes from healthy individuals (Howe 1998, Aretz 2007, Calva-Cerqueira 2009, Pinitiliciuc 2008, Piepoli 2012, Ngeow 2013, Burmester 2016). The variant was identified in dbSNP (rs80338965) as “with pathogenic allele, ClinVar (classified as pathogenic by Invitae, GeneDx, Ambry Genetics and 6 other submitters) and LOVD 3.0 (observed 76x). The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). In HEK-293T cells, expression of the variant decreased bone morphogenetic protein signaling (Carr 2012). The c.1245_1248del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 415 and leads to a premature stop codon at position 434. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the SMAD4 gene are an established mechanism of disease in juvenile polyposis syndrome and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -
Hereditary cancer-predisposing syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1
The c.1245_1248delCAGA pathogenic mutation, located in coding exon 9 of the SMAD4 gene, results from a deletion of four nucleotides between positions 1245 and 1248, causing a translational frameshift with a predicted alternate stop codon (p.D415Efs*20). This mutation has been reported in multiple individuals diagnosed with juvenile polyposis syndrome (JPS) (Aretz S et al. J. Med. Genet. 2007 Nov;44:702-9; Howe JR et al. Science. 1998 May;280:1086-8; Burmester JK et al. Dig Liver Dis. 2016 Oct;48:1255-9), multiple individuals with mixed polyposis, 4 of 5 whom had predominately juvenile polyps (Ngeow J et al. Gastroenterology. 2013 Jun;144:1402-9, 1409.e1-5), and in individuals diagnosed with JPS-hereditary hemorrhagic telangiectasia (JPS-HHT) (Teekakirikul P et al. Am. J. Med. Genet. A. 2013 Jan;161A:185-91; Heald B et al. Am. J. Med. Genet. A. 2015 Aug;167A:1758-62). A functional study showed this mutation leads to a 33% reduction in luciferase activity compared to wild-type, indicating that the mutation negatively impacted downstream bone morphogenetic protein (BMP) pathway signaling (Carr JC et al. J. Surg. Res. 2012 May;174:211-4). Of note, this alteration is also designated as 1244_7delACAG or 1372_1375del4 in published literature. In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -
Carcinoma of pancreas;C0796081:Myhre syndrome;C1832942:Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome;C1868081:Generalized juvenile polyposis/juvenile polyposis coli Pathogenic:1
SMAD4 NM_005359.5 exon 10 p.Asp415Glufs*20 (c.1245_1248delCAGA): This variant has been reported in the literature (alternate nomenclature: c.1244_1247del, c.1242_1245delAGAC, c.1372_1375del4) in multiple individuals with juvenile polyposis syndrome (JPS) (Howe 1998 PMID:9582123, Aretz 2007 PMID:17873119, Pintiliciuc 2008 PMID:18355998, Calva-Cerqueira 2009 PMID:18823382, Piepoli 2012 PMID:22748914, Ngeow 2013 PMID:23399955, Blatter 2015 PMID:26171675, Burmester 2016 PMID:27375208) and was shown to segregate with disease in several affected family members (Howe 1998 PMID:9582123, Piepoli 2012 PMID:22748914, Burmester 2016 PMID:27375208). This variant was also identified in an individual presenting with JPS, hereditary hemorrhagic telangiectasia (HTT), and features of syndromic TAAD (Teekakirikul 2013 PMID:23239472). This variant is not present in large control databases, and it is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:142253). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. However, an in vitro functional study showed significantly decreased luciferase activity with this deletion, which is suggested to have a negative impact on downstream BMP signaling (Carr 2012 PMID:22316667). However, these studies may not accurately represent in vivo biological function. This variant is a deletion of 4 nucleotides and creates a premature stop codon 20 amino acids downstream from this location which results in an absent or abnormal protein. Loss of function variants have been described as a mechanism of disease for this gene (Gallione 2010 PMID:20101697). In summary, this variant is classified as pathogenic based on the data above. -
Carcinoma of pancreas;C0345893:Juvenile polyposis syndrome;C0796081:Myhre syndrome;C1832942:Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome Pathogenic:1
SMAD4 NM_005359.5 exon 10 p.Asp415Glufs*20 (c.1245_1248delCAGA): This variant has been reported in the literature (alternate nomenclature: c.1244_1247del, c.1242_1245delAGAC, c.1372_1375del4) in multiple individuals with juvenile polyposis syndrome (JPS) (Howe 1998 PMID:9582123, Aretz 2007 PMID:17873119, Pintiliciuc 2008 PMID:18355998, Calva-Cerqueira 2009 PMID:18823382, Piepoli 2012 PMID:22748914, Ngeow 2013 PMID:23399955, Blatter 2015 PMID:26171675, Burmester 2016 PMID:27375208) and was shown to segregate with disease in several affected family members (Howe 1998 PMID:9582123, Piepoli 2012 PMID:22748914, Burmester 2016 PMID:27375208). This variant was also identified in an individual presenting with JPS, hereditary hemorrhagic telangiectasia (HTT), and features of syndromic TAAD (Teekakirikul 2013 PMID:23239472). This variant is not present in large control databases, and it is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:142253). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. However, an in vitro functional study showed significantly decreased luciferase activity with this deletion, which is suggested to have a negative impact on downstream BMP signaling (Carr 2012 PMID:22316667). However, these studies may not accurately represent in vivo biological function. This variant is a deletion of 4 nucleotides and creates a premature stop codon 20 amino acids downstream from this location which results in an absent or abnormal protein. Loss of function variants have been described as a mechanism of disease for this gene (Gallione 2010 PMID:20101697). In summary, this variant is classified as pathogenic based on the data above. -
Hereditary cancer-predisposing syndrome Pathogenic:1
This variant deletes 4 nucleotides in exon 10 of the SMAD4 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with juvenile polyposis syndrome (PMID: 9582123, 15235019, 16152648, 17873119, 18823382, 22748914, 23239472, 23399955) along with individuals affected with atypical forms of gastrointestinal polyposis (PMID: 18355998, 22748914, 23239472). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of SMAD4 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at