NM_001165963.4(SCN1A):c.3525dup (p.Glu1176Ter) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 9, 2020
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:: RCV001381928.6

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3525dup (p.Glu1176Ter)]

NM_001165963.4(SCN1A):c.3525dup (p.Glu1176Ter)

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.3525dup (p.Glu1176Ter)

HGVS:

NC_000002.12:g.166015633dup
NG_011906.1:g.63008dup
NM_001165963.4:c.3525dupMANE SELECT
NM_001165964.3:c.3441dup
NM_001202435.3:c.3525dup
NM_001353948.2:c.3525dup
NM_001353949.2:c.3492dup
NM_001353950.2:c.3492dup
NM_001353951.2:c.3492dup
NM_001353952.2:c.3492dup
NM_001353954.2:c.3489dup
NM_001353955.2:c.3489dup
NM_001353957.2:c.3441dup
NM_001353958.2:c.3441dup
NM_001353960.2:c.3438dup
NM_001353961.2:c.1083dup
NM_006920.6:c.3492dup
NP_001159435.1:p.Glu1176Ter
NP_001159436.1:p.Glu1148Ter
NP_001189364.1:p.Glu1176Ter
NP_001340877.1:p.Glu1176Ter
NP_001340878.1:p.Glu1165Ter
NP_001340879.1:p.Glu1165Ter
NP_001340880.1:p.Glu1165Ter
NP_001340881.1:p.Glu1165Ter
NP_001340883.1:p.Glu1164Ter
NP_001340884.1:p.Glu1164Ter
NP_001340886.1:p.Glu1148Ter
NP_001340887.1:p.Glu1148Ter
NP_001340889.1:p.Glu1147Ter
NP_001340890.1:p.Glu362Ter
NP_008851.3:p.Glu1165Ter
LRG_8:g.63008dup
NC_000002.11:g.166872141_166872142insA
NC_000002.11:g.166872143dup
NR_110598.1:n.196dup
NR_148667.2:n.3878dup

Protein change:

E1147*

Links:

dbSNP: rs2105628869

NCBI 1000 Genomes Browser:

rs2105628869

Molecular consequence:

NR_110598.1:n.196dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148667.2:n.3878dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001165963.4:c.3525dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001165964.3:c.3441dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001202435.3:c.3525dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353948.2:c.3525dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353949.2:c.3492dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353950.2:c.3492dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353951.2:c.3492dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353952.2:c.3492dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353954.2:c.3489dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353955.2:c.3489dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353957.2:c.3441dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353958.2:c.3441dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353960.2:c.3438dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001353961.2:c.1083dup - nonsense - [Sequence Ontology: SO:0001587]
NM_006920.6:c.3492dup - nonsense - [Sequence Ontology: SO:0001587]

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

Recent activity

Clear Turn Off Turn On

Gm34698 predicted gene, 34698 [Mus musculus]
Gm34698 predicted gene, 34698 [Mus musculus]
Gene ID:102638033

Gene
Gm34698 AND (alive[prop]) (1)
Gene
uncharacterized protein LOC111491196 [Cucurbita maxima]
uncharacterized protein LOC111491196 [Cucurbita maxima]
gi|1281022958|ref|XP_022995760.1|

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
SCV001580503	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 9, 2020)	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

SCV001580503

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 9, 2020)

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, SCV001580503.4

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

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SCN1A are known to be pathogenic (PMID: 17347258, 18930999). This variant has not been reported in the literature in individuals with SCN1A-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu1176*) in the SCN1A gene. It is expected to result in an absent or disrupted protein product.

#	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

ClinVar

Relating variation to medicine