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NM_000807.4(GABRA2):c.1060-5599C>T AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 21, 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:
RCV002895387.3

Allele description [Variation Report for NM_000807.4(GABRA2):c.1060-5599C>T]

NM_000807.4(GABRA2):c.1060-5599C>T

Gene:
GABRA2:gamma-aminobutyric acid type A receptor subunit alpha2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p12
Genomic location:
Preferred name:
NM_000807.4(GABRA2):c.1060-5599C>T
HGVS:
  • NC_000004.12:g.46256203G>A
  • NG_012835.2:g.138837C>T
  • NM_000807.4:c.1060-5599C>TMANE SELECT
  • NM_001114175.3:c.1060-5599C>T
  • NM_001286827.3:c.1066C>T
  • NM_001330690.2:c.1231C>T
  • NM_001377144.1:c.1231C>T
  • NM_001377145.1:c.1231C>T
  • NM_001377146.1:c.1060-5599C>T
  • NM_001377147.1:c.1060-5599C>T
  • NM_001377148.1:c.1060-5599C>T
  • NM_001377149.1:c.1060-5599C>T
  • NM_001377150.1:c.1060-5599C>T
  • NM_001377151.1:c.1060-5599C>T
  • NM_001377152.1:c.895-5599C>T
  • NM_001377153.1:c.895-5599C>T
  • NM_001377154.1:c.895-5599C>T
  • NP_001273756.1:p.Gln356Ter
  • NP_001317619.1:p.Gln411Ter
  • NP_001364073.1:p.Gln411Ter
  • NP_001364074.1:p.Gln411Ter
  • NC_000004.11:g.46258220G>A
Protein change:
Q356*
Molecular consequence:
  • NM_000807.4:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001114175.3:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377146.1:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377147.1:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377148.1:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377149.1:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377150.1:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377151.1:c.1060-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377152.1:c.895-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377153.1:c.895-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377154.1:c.895-5599C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001286827.3:c.1066C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001330690.2:c.1231C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001377144.1:c.1231C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001377145.1:c.1231C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003244641Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 21, 2022) 		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, SCV003244641.2

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with GABRA2-related conditions. 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. This sequence change creates a premature translational stop signal (p.Gln411*) in the GABRA2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 101 amino acid(s) of the GABRA2 protein.

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

Last Updated: Sep 29, 2024