NM_003072.5(SMARCA4):c.4200_4201delinsAC (p.Glu1401Gln) AND Rhabdoid tumor predisposition syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 17, 2022
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:: RCV002295949.4

Allele description [Variation Report for NM_003072.5(SMARCA4):c.4200_4201delinsAC (p.Glu1401Gln)]

NM_003072.5(SMARCA4):c.4200_4201delinsAC (p.Glu1401Gln)

Gene:

SMARCA4:SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_003072.5(SMARCA4):c.4200_4201delinsAC (p.Glu1401Gln)

HGVS:

NC_000019.10:g.11041336_11041337delinsAC
NG_011556.3:g.85405_85406delinsAC
NM_001128844.3:c.4200_4201delinsAC
NM_001128845.2:c.4110_4111delinsAC
NM_001128846.2:c.4110_4111delinsAC
NM_001128847.4:c.4101_4102delinsAC
NM_001128848.2:c.4101_4102delinsAC
NM_001128849.3:c.4296_4297delinsAC
NM_001374457.1:c.4101_4102delinsAC
NM_001387283.1:c.4296_4297delinsAC
NM_001411150.1:c.4197_4198delCGinsAC
NM_003072.5:c.4200_4201delinsACMANE SELECT
NP_001122316.1:p.Glu1401Gln
NP_001122317.1:p.Glu1371Gln
NP_001122318.1:p.Glu1371Gln
NP_001122319.1:p.Glu1368Gln
NP_001122320.1:p.Glu1368Gln
NP_001122321.1:p.Glu1433Gln
NP_001361386.1:p.Glu1368Gln
NP_001374212.1:p.Glu1433Gln
NP_001398079.1:p.Glu1400Gln
NP_003063.2:p.Glu1401Gln
LRG_878t1:c.4200_4201delinsAC
LRG_878:g.85405_85406delinsAC
LRG_878p1:p.Glu1401Gln
NC_000019.9:g.11152012_11152013delinsAC
NR_164683.1:n.4590_4591delinsAC

Protein change:

E1368Q

Molecular consequence:

NM_001128844.3:c.4200_4201delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001128845.2:c.4110_4111delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001128846.2:c.4110_4111delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001128847.4:c.4101_4102delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001128848.2:c.4101_4102delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001128849.3:c.4296_4297delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001374457.1:c.4101_4102delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001387283.1:c.4296_4297delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_001411150.1:c.4197_4198delCGinsAC - missense variant - [Sequence Ontology: SO:0001583]
NM_003072.5:c.4200_4201delinsAC - missense variant - [Sequence Ontology: SO:0001583]
NR_164683.1:n.4590_4591delinsAC - 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

Recent activity

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vacuolar cation/proton exchanger 3-like isoform X2 [Benincasa hispida]
vacuolar cation/proton exchanger 3-like isoform X2 [Benincasa hispida]
gi|1955831353|ref|XP_038904775.1|

Protein
vacuolar cation/proton exchanger 3-like [Cucurbita maxima]
vacuolar cation/proton exchanger 3-like [Cucurbita maxima]
gi|1281058526|ref|XP_022971605.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002596331	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002596331

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 17, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002596331.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with SMARCA4-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 1433 of the SMARCA4 protein (p.Glu1433Gln).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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