NM_198904.4(GABRG2):c.549-3T>G AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Oct 28, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001234167.2

Allele description [Variation Report for NM_198904.4(GABRG2):c.549-3T>G]

NM_198904.4(GABRG2):c.549-3T>G

Gene:
GABRG2:gamma-aminobutyric acid type A receptor subunit gamma2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q34
Genomic location:
Preferred name:
NM_198904.4(GABRG2):c.549-3T>G
HGVS:
  • NC_000005.10:g.162101232T>G
  • NG_009290.1:g.38591T>G
  • NM_000816.3:c.549-3T>G
  • NM_001375339.1:c.540-3T>G
  • NM_001375340.1:c.549-3T>G
  • NM_001375341.1:c.549-3T>G
  • NM_001375342.1:c.549-3T>G
  • NM_001375343.1:c.549-3T>G
  • NM_001375344.1:c.549-3T>G
  • NM_001375345.1:c.483-3T>G
  • NM_001375346.1:c.483-3T>G
  • NM_001375347.1:c.462-3T>G
  • NM_001375348.1:c.129-3T>G
  • NM_001375349.1:c.264-3T>G
  • NM_001375350.1:c.129-3T>G
  • NM_198903.2:c.549-3T>G
  • NM_198904.4:c.549-3T>GMANE SELECT
  • NC_000005.9:g.161528238T>G
Links:
dbSNP: rs750459631
NCBI 1000 Genomes Browser:
rs750459631
Molecular consequence:
  • NM_000816.3:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375339.1:c.540-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375340.1:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375341.1:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375342.1:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375343.1:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375344.1:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375345.1:c.483-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375346.1:c.483-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375347.1:c.462-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375348.1:c.129-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375349.1:c.264-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001375350.1:c.129-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_198903.2:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_198904.4:c.549-3T>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Epilepsy, childhood absence 2 (ECA2)
Identifiers:
MedGen: C1843244; Orphanet: 64280
Name:
Familial febrile seizures 8 (FEB8)
Synonyms:
CONVULSIONS, FAMILIAL FEBRILE, 8
Identifiers:
MONDO: MONDO:0011891; MedGen: C1969810; Orphanet: 36387; OMIM: 607681

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001406798Invitaecriteria provided, single submitter
Uncertain significance
(Oct 28, 2019)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Rare variants in γ-aminobutyric acid type A receptor genes in rolandic epilepsy and related syndromes.

Reinthaler EM, Dejanovic B, Lal D, Semtner M, Merkler Y, Reinhold A, Pittrich DA, Hotzy C, Feucht M, Steinböck H, Gruber-Sedlmayr U, Ronen GM, Neophytou B, Geldner J, Haberlandt E, Muhle H, Ikram MA, van Duijn CM, Uitterlinden AG, Hofman A, Altmüller J, Kawalia A, et al.

Ann Neurol. 2015 Jun;77(6):972-86. doi: 10.1002/ana.24395. Epub 2015 Mar 28.

PubMed [citation]
PMID:
25726841

Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy.

Bobbili DR, Lal D, May P, Reinthaler EM, Jabbari K, Thiele H, Nothnagel M, Jurkowski W, Feucht M, Nürnberg P, Lerche H, Zimprich F, Krause R, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Steinböck H, Neophytou B, Geldner J, Gruber-Sedlmayr U, Haberlandt E, et al.

Eur J Hum Genet. 2018 Feb;26(2):258-264. doi: 10.1038/s41431-017-0034-x. Epub 2018 Jan 22.

PubMed [citation]
PMID:
29358611
PMCID:
PMC5839048
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001406798.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change falls in intron 4 of the GABRG2 gene. It does not directly change the encoded amino acid sequence of the GABRG2 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs750459631, ExAC 0.006%). This variant has been observed in individual(s) with Rolandic epilepsy (PMID: 25726841, 29358611). ClinVar contains an entry for this variant (Variation ID: 205543). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. 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.

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

Last Updated: Nov 20, 2021

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