NM_001330260.2(SCN8A):c.635_640del (p.Asp212_Leu213del) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 5, 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:: RCV003590418.2

Allele description [Variation Report for NM_001330260.2(SCN8A):c.635_640del (p.Asp212_Leu213del)]

NM_001330260.2(SCN8A):c.635_640del (p.Asp212_Leu213del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

12q13.13

Genomic location:

Preferred name:

NM_001330260.2(SCN8A):c.635_640del (p.Asp212_Leu213del)

HGVS:

NC_000012.12:g.51689025_51689030del
NG_021180.3:g.104068_104073del
NM_001177984.3:c.706+176_706+181del
NM_001330260.2:c.635_640delMANE SELECT
NM_001369788.1:c.635_640del
NM_014191.4:c.706+176_706+181del
NP_001317189.1:p.Asp212_Leu213del
NP_001356717.1:p.Asp212_Leu213del
LRG_1389t1:c.635_640del
LRG_1389t2:c.706+176_706+181del
LRG_1389:g.104068_104073del
LRG_1389p1:p.Asp212_Leu213del
NC_000012.11:g.52082806_52082811del
NC_000012.11:g.52082809_52082814del

Molecular consequence:

NM_001330260.2:c.635_640del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001369788.1:c.635_640del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001177984.3:c.706+176_706+181del - intron variant - [Sequence Ontology: SO:0001627]
NM_014191.4:c.706+176_706+181del - intron variant - [Sequence Ontology: SO:0001627]

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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Mus musculus FIP1 like 1 (S. cerevisiae) (Fip1l1), mRNA
Mus musculus FIP1 like 1 (S. cerevisiae) (Fip1l1), mRNA
gi|141802634|ref|NM_024183.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004330482	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 5, 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

SCV004330482

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 5, 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, SCV004330482.1

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

Description

The SCN8A gene has multiple clinically relevant transcripts. This variant occurs in alternate transcript NM_001330260.1, and corresponds to NM_014191.3:c.706+176_706+181del in the primary transcript. This variant, c.635_640del, results in the deletion of 2 amino acid(s) of the SCN8A protein (p.Asp212_Leu213del), 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 SCN8A-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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: Sep 29, 2024

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