NM_001165963.4(SCN1A):c.3971dup (p.Arg1325fs) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 28, 2018
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:: RCV000690701.9

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3971dup (p.Arg1325fs)]

NM_001165963.4(SCN1A):c.3971dup (p.Arg1325fs)

Genes:

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

Variant type:

Duplication

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.3971dup (p.Arg1325fs)

HGVS:

NC_000002.12:g.166009750dup
NG_011906.1:g.68890dup
NM_001165963.4:c.3971dupMANE SELECT
NM_001165964.3:c.3887dup
NM_001202435.3:c.3971dup
NM_001353948.2:c.3971dup
NM_001353949.2:c.3938dup
NM_001353950.2:c.3938dup
NM_001353951.2:c.3938dup
NM_001353952.2:c.3938dup
NM_001353954.2:c.3935dup
NM_001353955.2:c.3935dup
NM_001353957.2:c.3887dup
NM_001353958.2:c.3887dup
NM_001353960.2:c.3884dup
NM_001353961.2:c.1529dup
NM_006920.6:c.3938dup
NP_001159435.1:p.Arg1325fs
NP_001159436.1:p.Arg1297fs
NP_001189364.1:p.Arg1325fs
NP_001340877.1:p.Arg1325fs
NP_001340878.1:p.Arg1314fs
NP_001340879.1:p.Arg1314fs
NP_001340880.1:p.Arg1314fs
NP_001340881.1:p.Arg1314fs
NP_001340883.1:p.Arg1313fs
NP_001340884.1:p.Arg1313fs
NP_001340886.1:p.Arg1297fs
NP_001340887.1:p.Arg1297fs
NP_001340889.1:p.Arg1296fs
NP_001340890.1:p.Arg511fs
NP_008851.3:p.Arg1314fs
LRG_8:g.68890dup
NC_000002.11:g.166866259_166866260insA
NC_000002.11:g.166866260dup
NM_001165963.1:c.3971dupT
NR_148667.2:n.4324dup

Protein change:

R1296fs

Links:

dbSNP: rs1559140306

NCBI 1000 Genomes Browser:

rs1559140306

Molecular consequence:

NM_001165963.4:c.3971dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165964.3:c.3887dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001202435.3:c.3971dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353948.2:c.3971dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353949.2:c.3938dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353950.2:c.3938dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353951.2:c.3938dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353952.2:c.3938dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353954.2:c.3935dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353955.2:c.3935dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353957.2:c.3887dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353958.2:c.3887dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353960.2:c.3884dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353961.2:c.1529dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006920.6:c.3938dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148667.2:n.4324dup - 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
SCV000818401	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 28, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17347258, 18930999, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000818401

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 28, 2018)

germline

clinical testing

PubMed (3)
[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

The spectrum of SCN1A-related infantile epileptic encephalopathies.

Harkin LA, McMahon JM, Iona X, Dibbens L, Pelekanos JT, Zuberi SM, Sadleir LG, Andermann E, Gill D, Farrell K, Connolly M, Stanley T, Harbord M, Andermann F, Wang J, Batish SD, Jones JG, Seltzer WK, Gardner A; Infantile Epileptic Encephalopathy Referral Consortium., Sutherland G, Berkovic SF, et al.

Brain. 2007 Mar;130(Pt 3):843-52.

PubMed [citation]

PMID:: 17347258

Spectrum of SCN1A gene mutations associated with Dravet syndrome: analysis of 333 patients.

Depienne C, Trouillard O, Saint-Martin C, Gourfinkel-An I, Bouteiller D, Carpentier W, Keren B, Abert B, Gautier A, Baulac S, Arzimanoglou A, Cazeneuve C, Nabbout R, LeGuern E.

J Med Genet. 2009 Mar;46(3):183-91. doi: 10.1136/jmg.2008.062323. Epub 2008 Oct 17.

PubMed [citation]

PMID:: 18930999

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000818401.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Arg1325Lysfs*7) in the SCN1A gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in an individual affected with generalized epilepsy with febrile seizures plus¬†(PMID:¬†21488303).¬† This variant has also been reported as c.3972insT. Loss-of-function variants in SCN1A are known to be pathogenic (PMID: 17347258, 18930999). For these reasons, this variant has been classified as Pathogenic.

#	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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