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NM_005902.4(SMAD3):c.483del (p.Glu162fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 11, 2014
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:
RCV000199186.1

Allele description [Variation Report for NM_005902.4(SMAD3):c.483del (p.Glu162fs)]

NM_005902.4(SMAD3):c.483del (p.Glu162fs)

Gene:
SMAD3:SMAD family member 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
15q22.33
Genomic location:
Preferred name:
NM_005902.4(SMAD3):c.483del (p.Glu162fs)
HGVS:
  • NC_000015.10:g.67165335del
  • NG_011990.1:g.104479del
  • NM_001145102.2:c.168del
  • NM_001145103.2:c.351del
  • NM_005902.4:c.483delMANE SELECT
  • NP_001138574.1:p.Glu57fs
  • NP_001138575.1:p.Glu118fs
  • NP_005893.1:p.Glu162fs
  • NC_000015.9:g.67457673del
  • NM_005902.3:c.483delC
  • p.E162KfsX24
Protein change:
E118fs
Links:
dbSNP: rs863223771
NCBI 1000 Genomes Browser:
rs863223771
Molecular consequence:
  • NM_001145102.2:c.168del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001145103.2:c.351del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_005902.4:c.483del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000250803GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Sep 11, 2014)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000250803.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

c.483delC: p.Glu162LysfsX24 in exon 3 in the SMAD3 gene (NM_005902.3). The normal sequence with the base that is deleted in braces is: TCCC{C}GAAA. The c.483delC mutation in the SMAD3 gene has not been reported previously as a disease-causing mutation nor as a benign polymorphism, to our knowledge. The c.483delC mutation causes a frameshift starting with codon Glutamic acid 162, changes this amino acid to a Lysine residue and creates a premature Stop codon at position 24 of the new reading frame, denoted p.Glu162LysfsX24. This mutation is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.483delC mutation was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Other frameshift mutations in the SMAD3 gene have been reported in association with Loeys-Dietz syndrome type 3. We interpret c.483delC as a disease-causing mutation. This variant has been observed to be maternally inherited. This variant was found in SMAD3

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

Last Updated: Nov 5, 2022