NM_001165963.4(SCN1A):c.3886T>A (p.Leu1296Met) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 11, 2023
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:: RCV000636357.10

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3886T>A (p.Leu1296Met)]

NM_001165963.4(SCN1A):c.3886T>A (p.Leu1296Met)

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.3886T>A (p.Leu1296Met)

HGVS:

NC_000002.12:g.166009835A>T
NG_011906.1:g.68805T>A
NM_001165963.4:c.3886T>AMANE SELECT
NM_001165964.3:c.3802T>A
NM_001202435.3:c.3886T>A
NM_001353948.2:c.3886T>A
NM_001353949.2:c.3853T>A
NM_001353950.2:c.3853T>A
NM_001353951.2:c.3853T>A
NM_001353952.2:c.3853T>A
NM_001353954.2:c.3850T>A
NM_001353955.2:c.3850T>A
NM_001353957.2:c.3802T>A
NM_001353958.2:c.3802T>A
NM_001353960.2:c.3799T>A
NM_001353961.2:c.1444T>A
NM_006920.6:c.3853T>A
NP_001159435.1:p.Leu1296Met
NP_001159436.1:p.Leu1268Met
NP_001189364.1:p.Leu1296Met
NP_001340877.1:p.Leu1296Met
NP_001340878.1:p.Leu1285Met
NP_001340879.1:p.Leu1285Met
NP_001340880.1:p.Leu1285Met
NP_001340881.1:p.Leu1285Met
NP_001340883.1:p.Leu1284Met
NP_001340884.1:p.Leu1284Met
NP_001340886.1:p.Leu1268Met
NP_001340887.1:p.Leu1268Met
NP_001340889.1:p.Leu1267Met
NP_001340890.1:p.Leu482Met
NP_008851.3:p.Leu1285Met
LRG_8:g.68805T>A
NC_000002.11:g.166866345A>T
NM_001165963.1:c.3886T>A
NM_001165963.3:c.3886T>A
NR_148667.2:n.4239T>A

Protein change:

L1267M

Links:

dbSNP: rs375896308

NCBI 1000 Genomes Browser:

rs375896308

Molecular consequence:

NM_001165963.4:c.3886T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.3802T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.3886T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.3886T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.3853T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.3853T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.3853T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.3853T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.3850T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.3850T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.3802T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.3802T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.3799T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.1444T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.3853T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.4239T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:: Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:: MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000757796	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 11, 2023)	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

SCV000757796

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 11, 2023)

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, SCV000757796.6

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

#	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: Sep 29, 2024

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