NM_001165963.4(SCN1A):c.6006_6008del (p.Lys2002_Asp2003delinsAsn) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 30, 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:: RCV001315081.8

Allele description [Variation Report for NM_001165963.4(SCN1A):c.6006_6008del (p.Lys2002_Asp2003delinsAsn)]

NM_001165963.4(SCN1A):c.6006_6008del (p.Lys2002_Asp2003delinsAsn)

Genes:

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

Variant type:

Deletion

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.6006_6008del (p.Lys2002_Asp2003delinsAsn)

HGVS:

NC_000002.12:g.165991268_165991270del
NG_011906.1:g.87371_87373del
NM_001165963.4:c.6006_6008delMANE SELECT
NM_001165964.3:c.5922_5924del
NM_001202435.3:c.6006_6008del
NM_001353948.2:c.6006_6008del
NM_001353949.2:c.5973_5975del
NM_001353950.2:c.5973_5975del
NM_001353951.2:c.5973_5975del
NM_001353952.2:c.5973_5975del
NM_001353954.2:c.5970_5972del
NM_001353955.2:c.5970_5972del
NM_001353957.2:c.5922_5924del
NM_001353958.2:c.5922_5924del
NM_001353960.2:c.5919_5921del
NM_001353961.2:c.3564_3566del
NM_006920.6:c.5973_5975del
NP_001159435.1:p.Lys2002_Asp2003delinsAsn
NP_001159436.1:p.Lys1974_Asp1975delinsAsn
NP_001189364.1:p.Lys2002_Asp2003delinsAsn
NP_001340877.1:p.Lys2002_Asp2003delinsAsn
NP_001340878.1:p.Lys1991_Asp1992delinsAsn
NP_001340879.1:p.Lys1991_Asp1992delinsAsn
NP_001340880.1:p.Lys1991_Asp1992delinsAsn
NP_001340881.1:p.Lys1991_Asp1992delinsAsn
NP_001340883.1:p.Lys1990_Asp1991delinsAsn
NP_001340884.1:p.Lys1990_Asp1991delinsAsn
NP_001340886.1:p.Lys1974_Asp1975delinsAsn
NP_001340887.1:p.Lys1974_Asp1975delinsAsn
NP_001340889.1:p.Lys1973_Asp1974delinsAsn
NP_001340890.1:p.Lys1188_Asp1189delinsAsn
NP_008851.3:p.Lys1991_Asp1992delinsAsn
LRG_8:g.87371_87373del
NC_000002.11:g.166847777_166847779del
NC_000002.11:g.166847778_166847780del
NR_148667.2:n.6423_6425del

Links:

dbSNP: rs1689085952

NCBI 1000 Genomes Browser:

rs1689085952

Molecular consequence:

NM_001165963.4:c.6006_6008del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001165964.3:c.5922_5924del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001202435.3:c.6006_6008del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353948.2:c.6006_6008del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353949.2:c.5973_5975del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353950.2:c.5973_5975del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353951.2:c.5973_5975del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353952.2:c.5973_5975del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353954.2:c.5970_5972del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353955.2:c.5970_5972del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353957.2:c.5922_5924del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353958.2:c.5922_5924del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353960.2:c.5919_5921del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001353961.2:c.3564_3566del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_006920.6:c.5973_5975del - inframe_indel - [Sequence Ontology: SO:0001820]
NR_148667.2:n.6423_6425del - 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

Recent activity

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A-kinase anchor protein 8 isoform 2 [Mus musculus]
A-kinase anchor protein 8 isoform 2 [Mus musculus]
gi|1274096223|ref|NP_001344689.1|

Protein
Mus musculus unc-119 lipid binding chaperone (Unc119), transcript variant 2, mRN...
Mus musculus unc-119 lipid binding chaperone (Unc119), transcript variant 2, mRNA
gi|928589399|ref|NM_011676.3|

Nucleotide
LOC120196670 [Hibiscus syriacus]
LOC120196670 [Hibiscus syriacus]
Gene ID:120196670

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001505637	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 30, 2020)	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

SCV001505637

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 30, 2020)

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, SCV001505637.5

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

Description

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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 variant, c.6006_6008del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the SCN1A protein (p.Lys2002_Asp2003delinsAsn).

#	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: Feb 28, 2024

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