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NM_005359.6(SMAD4):c.498del (p.Phe166fs) AND Juvenile polyposis syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 27, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001044219.4

Allele description [Variation Report for NM_005359.6(SMAD4):c.498del (p.Phe166fs)]

NM_005359.6(SMAD4):c.498del (p.Phe166fs)

Gene:
SMAD4:SMAD family member 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
18q21.2
Genomic location:
Preferred name:
NM_005359.6(SMAD4):c.498del (p.Phe166fs)
HGVS:
  • NC_000018.10:g.51054824del
  • NG_013013.2:g.91785del
  • NM_005359.6:c.498delMANE SELECT
  • NP_005350.1:p.Phe166fs
  • LRG_318t1:c.498del
  • LRG_318:g.91785del
  • NC_000018.9:g.48581192del
  • NC_000018.9:g.48581194del
  • NM_005359.5:c.498del
Protein change:
F166fs
Links:
dbSNP: rs1909795937
NCBI 1000 Genomes Browser:
rs1909795937
Molecular consequence:
  • NM_005359.6:c.498del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Juvenile polyposis syndrome (JPS)
Synonyms:
Polyposis juvenile intestinal; Polyposis familial of entire gastrointestinal tract
Identifiers:
MONDO: MONDO:0017380; MedGen: C0345893; Orphanet: 2929; OMIM: 174900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001208004Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 27, 2019) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Vessels' morphology in SMAD4 and BMPR1A-related juvenile polyposis.

Handra-Luca A, Condroyer C, de Moncuit C, Tepper M, Fléjou JF, Thomas G, Olschwang S.

Am J Med Genet A. 2005 Oct 1;138A(2):113-7.

PubMed [citation]
PMID:
16152648

Mutation screening in juvenile polyposis syndrome.

Pyatt RE, Pilarski R, Prior TW.

J Mol Diagn. 2006 Feb;8(1):84-8.

PubMed [citation]
PMID:
16436638
PMCID:
PMC1867574
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001208004.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SMAD4 are known to be pathogenic (PMID: 16152648, 16436638, 22810475). This variant has not been reported in the literature in individuals with SMAD4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Phe166Leufs*36) in the SMAD4 gene. It is expected to result in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024