NM_000807.4(GABRA2):c.398A>G (p.Lys133Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 31, 2023
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:: RCV003877544.2

Allele description [Variation Report for NM_000807.4(GABRA2):c.398A>G (p.Lys133Arg)]

NM_000807.4(GABRA2):c.398A>G (p.Lys133Arg)

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.398A>G (p.Lys133Arg)

HGVS:

NC_000004.12:g.46312574T>C
NG_012835.2:g.82466A>G
NM_000807.4:c.398A>GMANE SELECT
NM_001114175.1:c.398A>G
NM_001114175.3:c.398A>G
NM_001286827.3:c.233A>G
NM_001330690.2:c.398A>G
NM_001377144.1:c.398A>G
NM_001377145.1:c.398A>G
NM_001377146.1:c.398A>G
NM_001377147.1:c.398A>G
NM_001377148.1:c.398A>G
NM_001377149.1:c.398A>G
NM_001377150.1:c.398A>G
NM_001377151.1:c.398A>G
NM_001377152.1:c.233A>G
NM_001377153.1:c.233A>G
NM_001377154.1:c.233A>G
NM_001377155.1:c.398A>G
NP_000798.2:p.Lys133Arg
NP_001107647.1:p.Lys133Arg
NP_001273756.1:p.Lys78Arg
NP_001317619.1:p.Lys133Arg
NP_001364073.1:p.Lys133Arg
NP_001364074.1:p.Lys133Arg
NP_001364075.1:p.Lys133Arg
NP_001364076.1:p.Lys133Arg
NP_001364077.1:p.Lys133Arg
NP_001364078.1:p.Lys133Arg
NP_001364079.1:p.Lys133Arg
NP_001364080.1:p.Lys133Arg
NP_001364081.1:p.Lys78Arg
NP_001364082.1:p.Lys78Arg
NP_001364083.1:p.Lys78Arg
NP_001364084.1:p.Lys133Arg
NC_000004.11:g.46314591T>C

Protein change:

K133R

Molecular consequence:

NM_000807.4:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001114175.3:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001286827.3:c.233A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330690.2:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377144.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377145.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377146.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377147.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377148.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377149.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377150.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377151.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377152.1:c.233A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377153.1:c.233A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377154.1:c.233A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377155.1:c.398A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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tumor protein D53 isoform 5 [Mus musculus]
tumor protein D53 isoform 5 [Mus musculus]
gi|2707165412|ref|NP_001415796.1|

Protein
Mus musculus polypeptide GalNAc transferase-T2 mRNA, complete cds
Mus musculus polypeptide GalNAc transferase-T2 mRNA, complete cds
gi|13650038|gb|AF348968.1|

Nucleotide
tumor protein D53 isoform 1 [Mus musculus]
tumor protein D53 isoform 1 [Mus musculus]
gi|1318663316|ref|NP_001346293.1|

Protein
LOC130006625 [Homo sapiens]
LOC130006625 [Homo sapiens]
Gene ID:130006625

Gene
LOC130006622 [Homo sapiens]
LOC130006622 [Homo sapiens]
Gene ID:130006622

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004684189	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 31, 2023)	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

SCV004684189

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 31, 2023)

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, SCV004684189.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 133 of the GABRA2 protein (p.Lys133Arg). 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.

#	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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