NM_001330260.2(SCN8A):c.772A>G (p.Thr258Ala) AND Developmental and epileptic encephalopathy, 13

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2022
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:: RCV002283996.1

Allele description [Variation Report for NM_001330260.2(SCN8A):c.772A>G (p.Thr258Ala)]

NM_001330260.2(SCN8A):c.772A>G (p.Thr258Ala)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.13

Genomic location:

Preferred name:

NM_001330260.2(SCN8A):c.772A>G (p.Thr258Ala)

HGVS:

NC_000012.12:g.51699635A>G
NG_021180.3:g.114678A>G
NM_001177984.3:c.772A>G
NM_001330260.2:c.772A>GMANE SELECT
NM_001369788.1:c.772A>G
NM_014191.4:c.772A>G
NP_001171455.1:p.Thr258Ala
NP_001317189.1:p.Thr258Ala
NP_001356717.1:p.Thr258Ala
NP_055006.1:p.Thr258Ala
LRG_1389t1:c.772A>G
LRG_1389t2:c.772A>G
LRG_1389:g.114678A>G
LRG_1389p1:p.Thr258Ala
LRG_1389p2:p.Thr258Ala
NC_000012.11:g.52093419A>G

Protein change:

T258A

Molecular consequence:

NM_001177984.3:c.772A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330260.2:c.772A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369788.1:c.772A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_014191.4:c.772A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Developmental and epileptic encephalopathy, 13 (DEE13)
Synonyms:: Early infantile epileptic encephalopathy 13; SCN8A-Related Epilepsy
Identifiers:: MONDO: MONDO:0013801; MedGen: C3281191; Orphanet: 442835; OMIM: 614558

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Protein
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Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002573290	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 1, 2022)	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

SCV002573290

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 1, 2022)

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	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV002573290.1

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

Description

The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.95; 3Cnet: 0.97). A different missense change at the same codon (p.Thr258Ile) has been reported to be associated with SCN8A-related disorder (ClinVar ID: VCV000559632). However, as the evidence of pathogenicity is insufficient at this time, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Aug 5, 2023

ClinVar

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