VCV001709991.2 - ClinVar

NM_198904.4(GABRG2):c.941C>A (p.Thr314Lys)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_198904.4(GABRG2):c.941C>A (p.Thr314Lys)

Variation ID: 1709991 Accession: VCV001709991.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 5q34 5: 162149126 (GRCh38) [ NCBI UCSC ] 5: 161576132 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 15, 2022	Feb 28, 2024	May 11, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_198904.4:c.941C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_944494.1:p.Thr314Lys	missense
NM_000816.3:c.941C>A	NP_000807.2:p.Thr314Lys	missense
NM_001375339.1:c.932C>A	NP_001362268.1:p.Thr311Lys	missense
NM_001375340.1:c.923-2604C>A		intron variant
NM_001375341.1:c.938C>A	NP_001362270.1:p.Thr313Lys	missense
NM_001375342.1:c.938C>A	NP_001362271.1:p.Thr313Lys	missense
NM_001375343.1:c.1061C>A	NP_001362272.1:p.Thr354Lys	missense
NM_001375344.1:c.980C>A	NP_001362273.1:p.Thr327Lys	missense
NM_001375345.1:c.875C>A	NP_001362274.1:p.Thr292Lys	missense
NM_001375346.1:c.875C>A	NP_001362275.1:p.Thr292Lys	missense
NM_001375347.1:c.854C>A	NP_001362276.1:p.Thr285Lys	missense
NM_001375348.1:c.521C>A	NP_001362277.1:p.Thr174Lys	missense
NM_001375349.1:c.656C>A	NP_001362278.1:p.Thr219Lys	missense
NM_001375350.1:c.521C>A	NP_001362279.1:p.Thr174Lys	missense
NM_198903.2:c.1061C>A	NP_944493.2:p.Thr354Lys	missense
NC_000005.10:g.162149126C>A
NC_000005.9:g.161576132C>A
NG_009290.1:g.86485C>A

... more HGVS ... less HGVS

Protein change

T174K, T219K, T285K, T292K, T311K, T313K, T314K, T327K, T354K

Other names

Canonical SPDI

NC_000005.10:162149125:C:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
GABRG2		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	674	710

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Febrile seizures, familial, 8	Uncertain significance (1)	criteria provided, single submitter	Sep 3, 2021	RCV002290333.2
Epilepsy, childhood absence 2 Febrile seizures, familial, 8	Likely pathogenic (1)	criteria provided, single submitter	May 11, 2023	RCV003774967.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Sep 03, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Febrile seizures, familial, 8 Affected status: yes Allele origin: germline	MGZ Medical Genetics Center Accession: SCV002580377.1 First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022 Comment: ACMG criteria applied: PS2_MOD, PM1_SUP, PM2_SUP, PP3	Number of individuals with the variant: 1 Sex: female
Likely pathogenic (May 11, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Febrile seizures, familial, 8 Epilepsy, childhood absence 2 Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004596003.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Comment: This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional … (more) This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Thr314 amino acid residue in GABRG2. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GABRG2 protein function. ClinVar contains an entry for this variant (Variation ID: 1709991). This missense change has been observed in individual(s) with clinical features of GABRG2-related conditions (Invitae). This sequence change replaces threonine, which is neutral and polar, with lysine, which is basic and polar, at codon 314 of the GABRG2 protein (p.Thr314Lys). (less)

Comment:

This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Thr314 amino acid residue in GABRG2. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GABRG2 protein function. ClinVar contains an entry for this variant (Variation ID: 1709991). This missense change has been observed in individual(s) with clinical features of GABRG2-related conditions (Invitae). This sequence change replaces threonine, which is neutral and polar, with lysine, which is basic and polar, at codon 314 of the GABRG2 protein (p.Thr314Lys).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_198904.4(GABRG2):c.941C>A (p.Thr314Lys)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...