NM_001165963.4(SCN1A):c.632del (p.Asn211fs) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 13, 2021
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:: RCV002903398.3

Allele description [Variation Report for NM_001165963.4(SCN1A):c.632del (p.Asn211fs)]

NM_001165963.4(SCN1A):c.632del (p.Asn211fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.632del (p.Asn211fs)

HGVS:

NC_000002.12:g.166052915del
NG_011906.1:g.25726del
NM_001165963.4:c.632delMANE SELECT
NM_001165964.3:c.632del
NM_001202435.3:c.632del
NM_001353948.2:c.632del
NM_001353949.2:c.632del
NM_001353950.2:c.632del
NM_001353951.2:c.632del
NM_001353952.2:c.632del
NM_001353954.2:c.632del
NM_001353955.2:c.632del
NM_001353957.2:c.632del
NM_001353958.2:c.632del
NM_001353960.2:c.632del
NM_001353961.2:c.-1794del
NM_006920.6:c.632del
NP_001159435.1:p.Asn211fs
NP_001159436.1:p.Asn211fs
NP_001189364.1:p.Asn211fs
NP_001340877.1:p.Asn211fs
NP_001340878.1:p.Asn211fs
NP_001340879.1:p.Asn211fs
NP_001340880.1:p.Asn211fs
NP_001340881.1:p.Asn211fs
NP_001340883.1:p.Asn211fs
NP_001340884.1:p.Asn211fs
NP_001340886.1:p.Asn211fs
NP_001340887.1:p.Asn211fs
NP_001340889.1:p.Asn211fs
NP_008851.3:p.Asn211Metfs
NP_008851.3:p.Asn211fs
LRG_8t1:c.631del
LRG_8:g.25726del
LRG_8p1:p.Asn211Metfs
NC_000002.11:g.166909424del
NC_000002.11:g.166909425del
NM_006920.4:c.631delA
NR_148667.2:n.1018del

Protein change:

N211fs

Molecular consequence:

NM_001353961.2:c.-1794del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001165963.4:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165964.3:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001202435.3:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353948.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353949.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353950.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353951.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353952.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353954.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353955.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353957.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353958.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353960.2:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006920.6:c.632del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148667.2:n.1018del - 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
SCV003248990	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 13, 2021)	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

SCV003248990

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 13, 2021)

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, SCV003248990.2

#	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. This variant has not been reported in the literature in individuals affected with SCN1A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asn211Metfs*5) in the SCN1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SCN1A are known to be pathogenic (PMID: 17347258, 18930999).

#	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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