NC_000002.11:g.(?_165946660)_(167168266_?)del AND Early infantile epileptic encephalopathy with suppression bursts

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 8, 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:: RCV001390921.2

Allele description

NC_000002.11:g.(?_165946660)_(167168266_?)del

Genes:

CSRNP3:cysteine and serine rich nuclear protein 3 [Gene - OMIM - HGNC]
GALNT3:polypeptide N-acetylgalactosaminyltransferase 3 [Gene - OMIM - HGNC]
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
SCN3A:sodium voltage-gated channel alpha subunit 3 [Gene - OMIM - HGNC]
SCN9A:sodium voltage-gated channel alpha subunit 9 [Gene - OMIM - HGNC]
TTC21B:tetratricopeptide repeat domain 21B [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q24.3

Genomic location:

Chr2: 165946660 - 167168266 (on Assembly GRCh37)

Preferred name:

NC_000002.11:g.(?_165946660)_(167168266_?)del

HGVS:

NC_000002.11:g.(?_165946660)_(167168266_?)del

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
SCV001592800	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 8, 2020)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 17561957, 16865694, 20522430, 21719429, 26068938, 17347258, 18930999, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001592800

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 8, 2020)

germline

clinical testing

PubMed (8)
[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

Idiopathic epilepsies with seizures precipitated by fever and SCN1A abnormalities.

Marini C, Mei D, Temudo T, Ferrari AR, Buti D, Dravet C, Dias AI, Moreira A, Calado E, Seri S, Neville B, Narbona J, Reid E, Michelucci R, Sicca F, Cross HJ, Guerrini R.

Epilepsia. 2007 Sep;48(9):1678-1685. doi: 10.1111/j.1528-1167.2007.01122.x. Epub 2007 Jun 11.

PubMed [citation]

PMID:: 17561957

Microdeletions involving the SCN1A gene may be common in SCN1A-mutation-negative SMEI patients.

Suls A, Claeys KG, Goossens D, Harding B, Van Luijk R, Scheers S, Deprez L, Audenaert D, Van Dyck T, Beeckmans S, Smouts I, Ceulemans B, Lagae L, Buyse G, Barisic N, Misson JP, Wauters J, Del-Favero J, De Jonghe P, Claes LR.

Hum Mutat. 2006 Sep;27(9):914-20.

PubMed [citation]

PMID:: 16865694

See all PubMed Citations (8)

Details of each submission

From Invitae, SCV001592800.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the SCN1A gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has been observed in individual(s) with Dravet syndrome (PMID: 17561957, 16865694, 20522430, 21719429, 26068938). In at least one individual the variant was observed to be de novo. 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: Nov 11, 2023

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