NM_001165963.4(SCN1A):c.5066T>C (p.Met1689Thr) AND Generalized epilepsy with febrile seizures plus, type 2

Clinical significance:Likely pathogenic (Last evaluated: May 3, 2019)
Review status:1 star out of maximum of 4 stars
criteria provided, single submitter

Based on:: 1 submission [Details]
Record status:: current
Accession:: RCV000770782.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5066T>C (p.Met1689Thr)]

NM_001165963.4(SCN1A):c.5066T>C (p.Met1689Thr)

Genes:

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.5066T>C (p.Met1689Thr)

HGVS:

NC_000002.12:g.165992209A>G
NG_011906.1:g.86431T>C
NM_001165963.4:c.5066T>CMANE SELECT
NM_001165964.3:c.4982T>C
NM_001202435.3:c.5066T>C
NM_001353948.2:c.5066T>C
NM_001353949.2:c.5033T>C
NM_001353950.2:c.5033T>C
NM_001353951.2:c.5033T>C
NM_001353952.2:c.5033T>C
NM_001353954.2:c.5030T>C
NM_001353955.2:c.5030T>C
NM_001353957.2:c.4982T>C
NM_001353958.2:c.4982T>C
NM_001353960.2:c.4979T>C
NM_001353961.2:c.2624T>C
NM_006920.6:c.5033T>C
NP_001159435.1:p.Met1689Thr
NP_001159436.1:p.Met1661Thr
NP_001189364.1:p.Met1689Thr
NP_001340877.1:p.Met1689Thr
NP_001340878.1:p.Met1678Thr
NP_001340879.1:p.Met1678Thr
NP_001340880.1:p.Met1678Thr
NP_001340881.1:p.Met1678Thr
NP_001340883.1:p.Met1677Thr
NP_001340884.1:p.Met1677Thr
NP_001340886.1:p.Met1661Thr
NP_001340887.1:p.Met1661Thr
NP_001340889.1:p.Met1660Thr
NP_001340890.1:p.Met875Thr
NP_008851.3:p.Met1678Thr
LRG_8:g.86431T>C
NC_000002.11:g.166848719A>G
NM_001165963.1:c.5066T>C
NM_001165963.2:c.5066T>C
NR_148667.2:n.5483T>C

Protein change:

M1660T

Links:

Molecular consequence:

NM_001165963.4:c.5066T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.4982T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.5066T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.5066T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.5033T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.5033T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.5033T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.5033T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.5030T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.5030T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.4982T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.4982T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.4979T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.2624T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.5033T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.5483T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Generalized epilepsy with febrile seizures plus, type 2 (GEFSP2)
Synonyms:: GEFS+, TYPE 2
Identifiers:: MONDO: MONDO:0011461; MedGen: C1858673; Orphanet: 36387; OMIM: 604403

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000902247	Génétique des Maladies du Développement, Hospices Civils de Lyon	criteria provided, single submitter ACMG Guidelines, 2015	Likely pathogenic (May 3, 2019)	maternal	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

SCV000902247

Génétique des Maladies du Développement, Hospices Civils de Lyon

criteria provided, single submitter

ACMG Guidelines, 2015

Likely pathogenic
(May 3, 2019)

maternal

clinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

Help

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Génétique des Maladies du Développement, Hospices Civils de Lyon, SCV000902247.1

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

Description

Familial segregation

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

Last Updated: Feb 7, 2023

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