NM_001165963.4(SCN1A):c.3924A>T (p.Glu1308Asp) AND not specified

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Oct 31, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000188828.19

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3924A>T (p.Glu1308Asp)]

NM_001165963.4(SCN1A):c.3924A>T (p.Glu1308Asp)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.3924A>T (p.Glu1308Asp)

Other names:

p.E1308D:GAA>GAT

HGVS:

NC_000002.12:g.166009797T>A
NG_011906.1:g.68843A>T
NM_001165963.4:c.3924A>TMANE SELECT
NM_001165963.4:c.3924A>T
NM_001165964.3:c.3840A>T
NM_001202435.1:c.3924A>T
NM_001202435.3:c.3924A>T
NM_001353948.2:c.3924A>T
NM_001353949.2:c.3891A>T
NM_001353950.2:c.3891A>T
NM_001353951.2:c.3891A>T
NM_001353952.2:c.3891A>T
NM_001353954.2:c.3888A>T
NM_001353955.2:c.3888A>T
NM_001353957.2:c.3840A>T
NM_001353958.2:c.3840A>T
NM_001353960.2:c.3837A>T
NM_001353961.2:c.1482A>T
NM_006920.6:c.3891A>T
NP_001159435.1:p.Glu1308Asp
NP_001159436.1:p.Glu1280Asp
NP_001189364.1:p.Glu1308Asp
NP_001340877.1:p.Glu1308Asp
NP_001340878.1:p.Glu1297Asp
NP_001340879.1:p.Glu1297Asp
NP_001340880.1:p.Glu1297Asp
NP_001340881.1:p.Glu1297Asp
NP_001340883.1:p.Glu1296Asp
NP_001340884.1:p.Glu1296Asp
NP_001340886.1:p.Glu1280Asp
NP_001340887.1:p.Glu1280Asp
NP_001340889.1:p.Glu1279Asp
NP_001340890.1:p.Glu494Asp
NP_008851.3:p.Glu1297Asp
LRG_8t1:c.3891A>T
LRG_8:g.68843A>T
NC_000002.11:g.166866307T>A
NC_000002.12:g.166009797T>A
NM_001165963.1:c.3924A>T
NM_006920.4:c.3891A>T
NR_148667.2:n.4277A>T

Protein change:

E1279D

Links:

UniProtKB/Swiss-Prot: VAR_064257; dbSNP: rs121917910

NCBI 1000 Genomes Browser:

rs121917910

Molecular consequence:

NM_001165963.4:c.3924A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.3840A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.3924A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.3924A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.3891A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.3891A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.3891A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.3891A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.3888A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.3888A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.3840A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.3840A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.3837A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.1482A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.3891A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.4277A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000152607	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 3, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002600854	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Oct 31, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000152607

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 3, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002600854

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Oct 31, 2022)

germline

clinical testing

Citation Link

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
not provided	germline	no	not provided	not provided	not provided	not provided	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 Genetic Services Laboratory, University of Chicago, SCV000152607.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002600854.1

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

#	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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