NM_198904.4(GABRG2):c.1115A>G (p.Lys372Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 21, 2019
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:: RCV001049574.8

Allele description [Variation Report for NM_198904.4(GABRG2):c.1115A>G (p.Lys372Arg)]

NM_198904.4(GABRG2):c.1115A>G (p.Lys372Arg)

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.1115A>G (p.Lys372Arg)

HGVS:

NC_000005.10:g.162149300A>G
NG_009290.1:g.86659A>G
NM_000816.3:c.1115A>G
NM_001375339.1:c.1106A>G
NM_001375340.1:c.923-2430A>G
NM_001375341.1:c.1112A>G
NM_001375342.1:c.1112A>G
NM_001375343.1:c.1235A>G
NM_001375344.1:c.1154A>G
NM_001375345.1:c.1049A>G
NM_001375346.1:c.1049A>G
NM_001375347.1:c.1028A>G
NM_001375348.1:c.695A>G
NM_001375349.1:c.830A>G
NM_001375350.1:c.695A>G
NM_198903.2:c.1235A>G
NM_198904.4:c.1115A>GMANE SELECT
NP_000807.2:p.Lys372Arg
NP_001362268.1:p.Lys369Arg
NP_001362270.1:p.Lys371Arg
NP_001362271.1:p.Lys371Arg
NP_001362272.1:p.Lys412Arg
NP_001362273.1:p.Lys385Arg
NP_001362274.1:p.Lys350Arg
NP_001362275.1:p.Lys350Arg
NP_001362276.1:p.Lys343Arg
NP_001362277.1:p.Lys232Arg
NP_001362278.1:p.Lys277Arg
NP_001362279.1:p.Lys232Arg
NP_944493.2:p.Lys412Arg
NP_944494.1:p.Lys372Arg
NC_000005.9:g.161576306A>G

Protein change:

K232R

Links:

dbSNP: rs1765190002

NCBI 1000 Genomes Browser:

rs1765190002

Molecular consequence:

NM_001375340.1:c.923-2430A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000816.3:c.1115A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375339.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375341.1:c.1112A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375342.1:c.1112A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375343.1:c.1235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375344.1:c.1154A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375345.1:c.1049A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375346.1:c.1049A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375347.1:c.1028A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375348.1:c.695A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375349.1:c.830A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375350.1:c.695A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198903.2:c.1235A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198904.4:c.1115A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Epilepsy, childhood absence 2 (ECA2)
Identifiers:: MedGen: C1843244; Orphanet: 64280

Name:: Febrile seizures, familial, 8 (FEB8)
Synonyms:: CONVULSIONS, FAMILIAL FEBRILE, 8
Identifiers:: MONDO: MONDO:0011891; MedGen: C1969810; Orphanet: 36387; OMIM: 607681

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001213631	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 21, 2019)	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

SCV001213631

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 21, 2019)

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, SCV001213631.5

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

Description

This variant has not been reported in the literature in individuals with GABRG2-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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant is not present in population databases (ExAC no frequency). This sequence change replaces lysine with arginine at codon 372 of the GABRG2 protein (p.Lys372Arg). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and arginine.

#	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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