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NM_003072.5(SMARCA4):c.4209G>C (p.Glu1403Asp) AND Rhabdoid tumor predisposition syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 22, 2020
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:
RCV001056292.8

Allele description [Variation Report for NM_003072.5(SMARCA4):c.4209G>C (p.Glu1403Asp)]

NM_003072.5(SMARCA4):c.4209G>C (p.Glu1403Asp)

Gene:
SMARCA4:SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_003072.5(SMARCA4):c.4209G>C (p.Glu1403Asp)
HGVS:
  • NC_000019.10:g.11041345G>C
  • NG_011556.2:g.85424G>C
  • NM_001128844.3:c.4209G>C
  • NM_001128845.2:c.4119G>C
  • NM_001128846.2:c.4119G>C
  • NM_001128847.4:c.4110G>C
  • NM_001128848.2:c.4110G>C
  • NM_001128849.3:c.4305G>C
  • NM_001374457.1:c.4110G>C
  • NM_003072.5:c.4209G>CMANE SELECT
  • NP_001122316.1:p.Glu1403Asp
  • NP_001122317.1:p.Glu1373Asp
  • NP_001122318.1:p.Glu1373Asp
  • NP_001122319.1:p.Glu1370Asp
  • NP_001122320.1:p.Glu1370Asp
  • NP_001122321.1:p.Glu1435Asp
  • NP_001361386.1:p.Glu1370Asp
  • NP_003063.2:p.Glu1403Asp
  • LRG_878t1:c.4209G>C
  • LRG_878p1:p.Glu1403Asp
  • NC_000019.9:g.11152021G>C
  • NM_001128849.1:c.4305G>C
  • NR_164683.1:n.4599G>C
Protein change:
E1370D
Links:
dbSNP: rs2075598271
NCBI 1000 Genomes Browser:
rs2075598271
Molecular consequence:
  • NM_001128844.3:c.4209G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128845.2:c.4119G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128846.2:c.4119G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128847.4:c.4110G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128848.2:c.4110G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128849.3:c.4305G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374457.1:c.4110G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003072.5:c.4209G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_164683.1:n.4599G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Rhabdoid tumor predisposition syndrome 2 (RTPS2)
Identifiers:
MONDO: MONDO:0013224; MedGen: C2750074; Orphanet: 231108; Orphanet: 69077; OMIM: 613325

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001220728Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 22, 2020) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001220728.5

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SMARCA4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with aspartic acid at codon 1435 of the SMARCA4 protein (p.Glu1435Asp). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and aspartic acid.

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

Last Updated: Sep 29, 2024