NM_001330260.2(SCN8A):c.5904_5905del (p.Arg1968fs) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 27, 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:: RCV001997355.5

Allele description [Variation Report for NM_001330260.2(SCN8A):c.5904_5905del (p.Arg1968fs)]

NM_001330260.2(SCN8A):c.5904_5905del (p.Arg1968fs)

Gene:

SCN8A:sodium voltage-gated channel alpha subunit 8 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

12q13.13

Genomic location:

Preferred name:

NM_001330260.2(SCN8A):c.5904_5905del (p.Arg1968fs)

HGVS:

NC_000012.12:g.51807388AG[1]
NG_021180.3:g.222431AG[1]
NM_001177984.3:c.5781_5782del
NM_001330260.2:c.5904_5905delMANE SELECT
NM_001369788.1:c.5781_5782del
NM_014191.3:c.5904_5905del
NM_014191.4:c.5904_5905del
NP_001171455.1:p.Arg1927fs
NP_001317189.1:p.Arg1968fs
NP_001356717.1:p.Arg1927fs
NP_055006.1:p.Arg1968fs
LRG_1389t1:c.5904_5905del
LRG_1389t2:c.5904_5905del
LRG_1389:g.222431AG[1]
LRG_1389p1:p.Arg1968fs
LRG_1389p2:p.Arg1968fs
NC_000012.11:g.52201172AG[1]
NC_000012.11:g.52201172_52201173del

Protein change:

R1927fs

Links:

dbSNP: rs1938738246

NCBI 1000 Genomes Browser:

rs1938738246

Molecular consequence:

NM_001177984.3:c.5781_5782del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330260.2:c.5904_5905del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001369788.1:c.5781_5782del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014191.4:c.5904_5905del - frameshift variant - [Sequence Ontology: SO:0001589]

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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AGENCOURT_6543404 NIH_MGC_88 Homo sapiens cDNA clone IMAGE:5741062 5', mRNA sequ...
AGENCOURT_6543404 NIH_MGC_88 Homo sapiens cDNA clone IMAGE:5741062 5', mRNA sequence
gi|18783915|gnl|dbEST|11121130|gb|B 26.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002236586	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 27, 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

SCV002236586

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 27, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002236586.3

#	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 affected with SCN8A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change results in a frameshift in the SCN8A gene (p.Arg1968Serfs*29). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 13 amino acid(s) of the SCN8A protein and extend the protein by 15 additional amino acid residues.

#	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: Oct 8, 2024

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