rs377767373

Variant names:

• chr18-51078354-CAG-C
• rs377767373
• NM_005359.6:c.1549_1550delAG

Your query was ambiguous. Multiple possible variants found:

• chr18-51078354-CAG-C
• chr18-51078354-CAG-CAGAGAG

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PVS1_Strong PM2 PP5_Very_Strong

The NM_005359.6(SMAD4):​c.1549_1550delAG​(p.Ser517HisfsTer9) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SMAD4 NM_005359.6 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6
• 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

Our verdict: Pathogenic. The variant received 14 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 19 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 18-51078354-CAG-C is Pathogenic according to our data. Variant chr18-51078354-CAG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 545806.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.1549_1550delAG	p.Ser517HisfsTer9	frameshift_variant	Exon 12 of 12	ENST00000342988.8	NP_005350.1
SMAD4	NM_001407041.1	c.1549_1550delAG	p.Ser517HisfsTer9	frameshift_variant	Exon 12 of 12		NP_001393970.1
SMAD4	NM_001407042.1	c.1549_1550delAG	p.Ser517HisfsTer9	frameshift_variant	Exon 12 of 12		NP_001393971.1
SMAD4	NR_176265.1	n.2200_2201delAG		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.1549_1550delAG	p.Ser517HisfsTer9	frameshift_variant	Exon 12 of 12	5	NM_005359.6	ENSP00000341551.3

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Jul 25, 2017

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This deletion of two nucleotides in SMAD4 is denoted c.1549_1550delAG at the cDNA level and p.Ser517HisfsX9 (S517HfsX9) at the protein level. The normal sequence, with the bases that are deleted in brackets, is ACAG[delAG]CATC. The deletion causes a frameshift which changes a Serine to a Histidine at codon 517, and creates a premature stop codon at position 9 of the new reading frame. This variant is predicted to cause loss of normal protein function through protein truncation. SMAD4 Ser517HisfsX9, also known as c.(1546-1548)CAGfs using alternate nomenclature, has not, to our knowledge, been published in the literature as a germline variant; however, it has been reported as a somatic variant in a pancreatic tumor (Witkiewicz 2015). Based on the currently available information, we consider this deletion to be a likely pathogenic variant. -

Nov 15, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The SMAD4 c.1549_1550del (p.Ser517Hisfs*9) variant alters the translational reading frame of the SMAD4 mRNA and is predicted to cause the premature termination of SMAD4 protein synthesis. This variant has not been reported in individuals with SMAD4-related conditions in the published literature. However, it has been reported as a somatic variant in a pancreatic tumor (PMID: 25855536 (2015)). 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 likely pathogenic. -

Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome Pathogenic:2

Dec 23, 2024

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -

Aug 20, 2023

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Jun 12, 2019

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1549_1550delAG pathogenic mutation, located in coding exon 11 of the SMAD4 gene, results from a deletion of two nucleotides at nucleotide positions 1549 to 1550, causing a translational frameshift with a predicted alternate stop codon (p.S517Hfs*9). This alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation. -

Juvenile polyposis syndrome Pathogenic:1

Oct 10, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Ser517Hisfs*9) in the SMAD4 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 36 amino acid(s) of the SMAD4 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SMAD4-related conditions. ClinVar contains an entry for this variant (Variation ID: 545806). This variant disrupts a region of the SMAD4 protein in which other variant(s) (p.Ala532Profs*5) have been determined to be pathogenic (PMID: 15031030). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it 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
Mutation Taster		=0/200	disease causing (ClinVar)

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: rs377767373; hg19: chr18-48604724; COSMIC: COSV61688629; COSMIC: COSV61688629;