NM_003072.5(SMARCA4):c.4180G>A (p.Glu1394Lys) AND Rhabdoid tumor predisposition syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 8, 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:: RCV001862206.6

Allele description [Variation Report for NM_003072.5(SMARCA4):c.4180G>A (p.Glu1394Lys)]

NM_003072.5(SMARCA4):c.4180G>A (p.Glu1394Lys)

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.4180G>A (p.Glu1394Lys)

HGVS:

NC_000019.10:g.11041316G>A
NG_011556.2:g.85395G>A
NM_001128844.3:c.4180G>A
NM_001128845.2:c.4090G>A
NM_001128846.2:c.4090G>A
NM_001128847.4:c.4081G>A
NM_001128848.2:c.4081G>A
NM_001128849.3:c.4276G>A
NM_001374457.1:c.4081G>A
NM_003072.5:c.4180G>AMANE SELECT
NP_001122316.1:p.Glu1394Lys
NP_001122317.1:p.Glu1364Lys
NP_001122318.1:p.Glu1364Lys
NP_001122319.1:p.Glu1361Lys
NP_001122320.1:p.Glu1361Lys
NP_001122321.1:p.Glu1426Lys
NP_001361386.1:p.Glu1361Lys
NP_003063.2:p.Glu1394Lys
LRG_878t1:c.4180G>A
LRG_878p1:p.Glu1394Lys
NC_000019.9:g.11151992G>A
NC_000019.9:g.11151992G>A
NM_001128849.1:c.4276G>A
NR_164683.1:n.4570G>A

Protein change:

E1361K

Links:

dbSNP: rs1238368623

NCBI 1000 Genomes Browser:

rs1238368623

Molecular consequence:

NM_001128844.3:c.4180G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128845.2:c.4090G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128846.2:c.4090G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128847.4:c.4081G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128848.2:c.4081G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128849.3:c.4276G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374457.1:c.4081G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003072.5:c.4180G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164683.1:n.4570G>A - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002312460	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 8, 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

SCV002312460

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 8, 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, SCV002312460.3

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C55"). ClinVar contains an entry for this variant (Variation ID: 824746). This variant has not been reported in the literature in individuals affected with SMARCA4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1426 of the SMARCA4 protein (p.Glu1426Lys).

#	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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