NM_005097.4(LGI1):c.717A>C (p.Ile239=) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Dec 1, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000727013.18

Allele description [Variation Report for NM_005097.4(LGI1):c.717A>C (p.Ile239=)]

NM_005097.4(LGI1):c.717A>C (p.Ile239=)

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.717A>C (p.Ile239=)

Other names:

p.I239I:ATA>ATC

HGVS:

NC_000010.11:g.93793229A>C
NG_011832.1:g.40421A>C
NM_001308275.2:c.717A>C
NM_001308276.2:c.573A>C
NM_005097.4:c.717A>CMANE SELECT
NP_001295204.1:p.Ile239=
NP_001295205.1:p.Ile191=
NP_005088.1:p.Ile239=
NC_000010.10:g.95552986A>C
NM_005097.2:c.717A>C
NR_131777.2:n.854A>C

Links:

dbSNP: rs146425212

NCBI 1000 Genomes Browser:

rs146425212

Molecular consequence:

NR_131777.2:n.854A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001308275.2:c.717A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001308276.2:c.573A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_005097.4:c.717A>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000704920	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Uncertain significance (Jun 21, 2018)	germline	clinical testing	Citation Link,
SCV001144460	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely benign (Aug 30, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15079010, 26467025
SCV004698506	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Dec 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000704920

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Uncertain significance
(Jun 21, 2018)

germline

clinical testing

Citation Link,

SCV001144460

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely benign
(Aug 30, 2018)

germline

clinical testing

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

SCV004698506

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Dec 1, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

LGI1 mutations in temporal lobe epilepsies.

Berkovic SF, Izzillo P, McMahon JM, Harkin LA, McIntosh AM, Phillips HA, Briellmann RS, Wallace RH, Mazarib A, Neufeld MY, Korczyn AD, Scheffer IE, Mulley JC.

Neurology. 2004 Apr 13;62(7):1115-9.

PubMed [citation]

PMID:: 15079010

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Eurofins Ntd Llc (ga), SCV000704920.2

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

#	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		2	not provided	not provided	not provided

From Athena Diagnostics, SCV001144460.1

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

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004698506.8

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

Description

LGI1: BP4

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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