NM_005097.4(LGI1):c.836C>G (p.Thr279Arg) AND Autosomal dominant epilepsy with auditory features

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 4, 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:: RCV002232846.14

Allele description [Variation Report for NM_005097.4(LGI1):c.836C>G (p.Thr279Arg)]

NM_005097.4(LGI1):c.836C>G (p.Thr279Arg)

Gene:

LGI1:leucine rich glioma inactivated 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.33

Genomic location:

Preferred name:

NM_005097.4(LGI1):c.836C>G (p.Thr279Arg)

HGVS:

NC_000010.11:g.93793348C>G
NG_011832.1:g.40540C>G
NM_001308275.2:c.836C>G
NM_001308276.2:c.692C>G
NM_005097.4:c.836C>GMANE SELECT
NP_001295204.1:p.Thr279Arg
NP_001295205.1:p.Thr231Arg
NP_005088.1:p.Thr279Arg
NC_000010.10:g.95553105C>G
NM_005097.2:c.836C>G
NR_131777.2:n.973C>G

Protein change:

T231R

Links:

dbSNP: rs1159639109

NCBI 1000 Genomes Browser:

rs1159639109

Molecular consequence:

NM_001308275.2:c.836C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001308276.2:c.692C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005097.4:c.836C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_131777.2:n.973C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Autosomal dominant epilepsy with auditory features
Identifiers:: MONDO: MONDO:0010898; MedGen: C1838062

Recent activity

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650140[uid] AND (alive[prop]) (0)
Gene
Protein Links for Nucleotide (Select 2083593570) (2)
Protein
Klebsiella sp. CVUAS 10191.3 NODE_102, whole genome shotgun sequence
Klebsiella sp. CVUAS 10191.3 NODE_102, whole genome shotgun sequence
gi|2083593588|ref|NZ_PXNV01000102.1 |WGS:NZ_PXNV01|NODE_102

Nucleotide
Klebsiella sp. CVUAS 10191.3 NODE_97, whole genome shotgun sequence
Klebsiella sp. CVUAS 10191.3 NODE_97, whole genome shotgun sequence
gi|2083593583|ref|NZ_PXNV01000097.1 |WGS:NZ_PXNV01|NODE_97

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000813920	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 4, 2022)	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

SCV000813920

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 4, 2022)

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, SCV000813920.4

#	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 threonine, which is neutral and polar, with arginine, which is basic and polar, at codon 279 of the LGI1 protein (p.Thr279Arg). 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 566558). This variant has not been reported in the literature in individuals affected with LGI1-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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: Oct 26, 2024

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