NM_001165963.4(SCN1A):c.1323_1328del (p.Ala442_Glu443del) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 21, 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:: RCV001873585.5

Allele description [Variation Report for NM_001165963.4(SCN1A):c.1323_1328del (p.Ala442_Glu443del)]

NM_001165963.4(SCN1A):c.1323_1328del (p.Ala442_Glu443del)

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.1323_1328del (p.Ala442_Glu443del)

HGVS:

NC_000002.12:g.166046821_166046826del
NG_011906.1:g.31816_31821del
NM_001165963.4:c.1323_1328delMANE SELECT
NM_001165964.3:c.1323_1328del
NM_001202435.3:c.1323_1328del
NM_001353948.2:c.1323_1328del
NM_001353949.2:c.1323_1328del
NM_001353950.2:c.1323_1328del
NM_001353951.2:c.1323_1328del
NM_001353952.2:c.1323_1328del
NM_001353954.2:c.1323_1328del
NM_001353955.2:c.1323_1328del
NM_001353957.2:c.1323_1328del
NM_001353958.2:c.1323_1328del
NM_001353960.2:c.1323_1328del
NM_001353961.2:c.-1103_-1098del
NM_006920.6:c.1323_1328del
NP_001159435.1:p.Ala442_Glu443del
NP_001159436.1:p.Ala442_Glu443del
NP_001189364.1:p.Ala442_Glu443del
NP_001340877.1:p.Ala442_Glu443del
NP_001340878.1:p.Ala442_Glu443del
NP_001340879.1:p.Ala442_Glu443del
NP_001340880.1:p.Ala442_Glu443del
NP_001340881.1:p.Ala442_Glu443del
NP_001340883.1:p.Ala442_Glu443del
NP_001340884.1:p.Ala442_Glu443del
NP_001340886.1:p.Ala442_Glu443del
NP_001340887.1:p.Ala442_Glu443del
NP_001340889.1:p.Ala442_Glu443del
NP_008851.3:p.Ala442_Glu443del
LRG_8:g.31816_31821del
NC_000002.11:g.166903329_166903334del
NC_000002.11:g.166903331_166903336del
NR_148667.2:n.1709_1714del

Links:

dbSNP: rs1697886499

NCBI 1000 Genomes Browser:

rs1697886499

Molecular consequence:

NM_001353961.2:c.-1103_-1098del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001165963.4:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001165964.3:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001202435.3:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353948.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353949.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353950.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353951.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353952.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353954.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353955.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353957.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353958.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353960.2:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_006920.6:c.1323_1328del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_148667.2:n.1709_1714del - 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
SCV002221389	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 21, 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

SCV002221389

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 21, 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 Invitae, SCV002221389.3

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

Description

This variant, c.1323_1328del, results in the deletion of 2 amino acid(s) of the SCN1A protein (p.Ala442_Glu443del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SCN1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 916180). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Aug 4, 2024

ClinVar

Relating variation to medicine