NM_005097.4(LGI1):c.688C>T (p.Gln230Ter) AND Autosomal dominant epilepsy with auditory features

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 18, 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:: RCV002230371.12

Allele description [Variation Report for NM_005097.4(LGI1):c.688C>T (p.Gln230Ter)]

NM_005097.4(LGI1):c.688C>T (p.Gln230Ter)

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.688C>T (p.Gln230Ter)

HGVS:

NC_000010.11:g.93793200C>T
NG_011832.1:g.40392C>T
NM_001308275.2:c.688C>T
NM_001308276.2:c.544C>T
NM_005097.4:c.688C>TMANE SELECT
NP_001295204.1:p.Gln230Ter
NP_001295205.1:p.Gln182Ter
NP_005088.1:p.Gln230Ter
NC_000010.10:g.95552957C>T
NM_005097.2:c.688C>T
NR_131777.2:n.825C>T

Protein change:

Q182*

Links:

dbSNP: rs1060502054

NCBI 1000 Genomes Browser:

rs1060502054

Molecular consequence:

NR_131777.2:n.825C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001308275.2:c.688C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001308276.2:c.544C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_005097.4:c.688C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

inorganic pyrophosphatase 2, mitochondrial isoform 4 precursor [Homo sapiens]
inorganic pyrophosphatase 2, mitochondrial isoform 4 precursor [Homo sapiens]
gi|77812682|ref|NP_789843.2|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000548371	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 18, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24206907, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000548371

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 18, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Seizure semiology in autosomal dominant epilepsy with auditory features, due to novel LGI1 mutations.

Sadleir LG, Agher D, Chabrol E, Elkouby L, Leguern E, Paterson SJ, Harty R, Bellows ST, Berkovic SF, Scheffer IE, Baulac S.

Epilepsy Res. 2013 Dec;107(3):311-7. doi: 10.1016/j.eplepsyres.2013.09.008. Epub 2013 Oct 8.

PubMed [citation]

PMID:: 24206907

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, SCV000548371.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Gln230*) in the LGI1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LGI1 are known to be pathogenic (PMID: 24206907). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 408592). 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 13, 2024

ClinVar

Relating variation to medicine