NM_152743.4(BRAT1):c.1013dup (p.Gly339fs) AND Rigidity and multifocal seizure syndrome, lethal neonatal

Clinical significance:Pathogenic (Last evaluated: Jul 21, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000802074.1

Allele description [Variation Report for NM_152743.4(BRAT1):c.1013dup (p.Gly339fs)]

NM_152743.4(BRAT1):c.1013dup (p.Gly339fs)

Gene:
BRAT1:BRCA1 associated ATM activator 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
7p22.3
Genomic location:
Preferred name:
NM_152743.4(BRAT1):c.1013dup (p.Gly339fs)
HGVS:
  • NC_000007.14:g.2542126dup
  • NG_032167.1:g.18637dup
  • NM_001350626.2:c.1013dup
  • NM_001350627.2:c.488dup
  • NM_152743.4:c.1013dupMANE SELECT
  • NP_001337555.1:p.Gly339fs
  • NP_001337556.1:p.Gly164fs
  • NP_689956.2:p.Gly339fs
  • NC_000007.13:g.2581760dup
  • NM_152743.3:c.1013dupC
  • NR_146879.2:n.1072dup
Protein change:
G164fs
Links:
dbSNP: rs754341393
NCBI 1000 Genomes Browser:
rs754341393
Molecular consequence:
  • NM_001350626.2:c.1013dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001350627.2:c.488dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_152743.4:c.1013dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_146879.2:n.1072dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Rigidity and multifocal seizure syndrome, lethal neonatal (RMFSL)
Identifiers:
MONDO: MONDO:0013784; MedGen: C3281029; Orphanet: 435845; OMIM: 614498

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000941888Invitaecriteria provided, single submitter
Pathogenic
(Jul 21, 2018)
germlineclinical testing

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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000941888.1

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

Description

This sequence change creates a premature translational stop signal (p.Gly339Argfs*64) in the BRAT1 gene. It is expected to result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with BRAT1-related disease. Loss-of-function variants in BRAT1 are known to be pathogenic (PMID: 22279524, 25500575). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Aug 6, 2020

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