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NM_003072.5(SMARCA4):c.4243C>T (p.Arg1415Ter) AND Rhabdoid tumor predisposition syndrome 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 18, 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:
RCV000232997.7

Allele description [Variation Report for NM_003072.5(SMARCA4):c.4243C>T (p.Arg1415Ter)]

NM_003072.5(SMARCA4):c.4243C>T (p.Arg1415Ter)

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.4243C>T (p.Arg1415Ter)
HGVS:
  • NC_000019.10:g.11041379C>T
  • NG_011556.3:g.85448C>T
  • NM_001128844.3:c.4243C>T
  • NM_001128845.2:c.4153C>T
  • NM_001128846.2:c.4153C>T
  • NM_001128847.4:c.4144C>T
  • NM_001128848.2:c.4144C>T
  • NM_001128849.3:c.4339C>T
  • NM_001374457.1:c.4144C>T
  • NM_001387283.1:c.4339C>T
  • NM_003072.5:c.4243C>TMANE SELECT
  • NP_001122316.1:p.Arg1415Ter
  • NP_001122317.1:p.Arg1385Ter
  • NP_001122318.1:p.Arg1385Ter
  • NP_001122319.1:p.Arg1382Ter
  • NP_001122320.1:p.Arg1382Ter
  • NP_001122321.1:p.Arg1447Ter
  • NP_001361386.1:p.Arg1382Ter
  • NP_001374212.1:p.Arg1447Ter
  • NP_003063.2:p.Arg1415Ter
  • LRG_878t1:c.4243C>T
  • LRG_878:g.85448C>T
  • LRG_878p1:p.Arg1415Ter
  • NC_000019.9:g.11152055C>T
  • NG_011556.2:g.85458C>T
  • NM_001128849.1:c.4339C>T
  • NR_164683.1:n.4633C>T
Protein change:
R1382*
Links:
dbSNP: rs878854224
NCBI 1000 Genomes Browser:
rs878854224
Molecular consequence:
  • NR_164683.1:n.4633C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001128844.3:c.4243C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001128845.2:c.4153C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001128846.2:c.4153C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001128847.4:c.4144C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001128848.2:c.4144C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001128849.3:c.4339C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374457.1:c.4144C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001387283.1:c.4339C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_003072.5:c.4243C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000286085Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 18, 2020) 		germlineclinical testing

PubMed (3)
[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

Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.

Ramos P, Karnezis AN, Craig DW, Sekulic A, Russell ML, Hendricks WP, Corneveaux JJ, Barrett MT, Shumansky K, Yang Y, Shah SP, Prentice LM, Marra MA, Kiefer J, Zismann VL, McEachron TA, Salhia B, Prat J, D'Angelo E, Clarke BA, Pressey JG, Farley JH, et al.

Nat Genet. 2014 May;46(5):427-9. doi: 10.1038/ng.2928. Epub 2014 Mar 23.

PubMed [citation]
PMID:
24658001
PMCID:
PMC4332808

Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type.

Witkowski L, Carrot-Zhang J, Albrecht S, Fahiminiya S, Hamel N, Tomiak E, Grynspan D, Saloustros E, Nadaf J, Rivera B, Gilpin C, Castellsagué E, Silva-Smith R, Plourde F, Wu M, Saskin A, Arseneault M, Karabakhtsian RG, Reilly EA, Ueland FR, Margiolaki A, Pavlakis K, et al.

Nat Genet. 2014 May;46(5):438-43. doi: 10.1038/ng.2931. Epub 2014 Mar 23.

PubMed [citation]
PMID:
24658002
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000286085.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant has not been reported in the literature in individuals with SMARCA4-related conditions. ClinVar contains an entry for this variant (Variation ID: 238464). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg1447*) in the SMARCA4 gene. It is expected to result in an absent or disrupted protein product. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SMARCA4 are known to be pathogenic (PMID: 24658001, 24658002).

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

Last Updated: Sep 29, 2024