NM_001165963.4(SCN1A):c.4884T>A (p.Tyr1628Ter) AND Generalized epilepsy with febrile seizures plus, type 2

Germline classification:: Uncertain significance (1 submission)
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:: RCV002510640.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.4884T>A (p.Tyr1628Ter)]

NM_001165963.4(SCN1A):c.4884T>A (p.Tyr1628Ter)

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.4884T>A (p.Tyr1628Ter)

HGVS:

NC_000002.12:g.165992391A>T
NG_011906.1:g.86249T>A
NM_001165963.4:c.4884T>AMANE SELECT
NM_001165964.3:c.4800T>A
NM_001202435.3:c.4884T>A
NM_001353948.2:c.4884T>A
NM_001353949.2:c.4851T>A
NM_001353950.2:c.4851T>A
NM_001353951.2:c.4851T>A
NM_001353952.2:c.4851T>A
NM_001353954.2:c.4848T>A
NM_001353955.2:c.4848T>A
NM_001353957.2:c.4800T>A
NM_001353958.2:c.4800T>A
NM_001353960.2:c.4797T>A
NM_001353961.2:c.2442T>A
NM_006920.6:c.4851T>A
NP_001159435.1:p.Tyr1628Ter
NP_001159436.1:p.Tyr1600Ter
NP_001189364.1:p.Tyr1628Ter
NP_001340877.1:p.Tyr1628Ter
NP_001340878.1:p.Tyr1617Ter
NP_001340879.1:p.Tyr1617Ter
NP_001340880.1:p.Tyr1617Ter
NP_001340881.1:p.Tyr1617Ter
NP_001340883.1:p.Tyr1616Ter
NP_001340884.1:p.Tyr1616Ter
NP_001340886.1:p.Tyr1600Ter
NP_001340887.1:p.Tyr1600Ter
NP_001340889.1:p.Tyr1599Ter
NP_001340890.1:p.Tyr814Ter
NP_008851.3:p.Tyr1617Ter
NP_008851.3:p.Tyr1617Ter
LRG_8t1:c.4851T>A
LRG_8:g.86249T>A
LRG_8p1:p.Tyr1617Ter
NC_000002.11:g.166848901A>T
NM_001165963.3:c.4884T>A
NM_006920.4:c.4851T>A
NR_148667.2:n.5301T>A

Protein change:

Y1599*

Molecular consequence:

NR_148667.2:n.5301T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001165963.4:c.4884T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001165964.3:c.4800T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001202435.3:c.4884T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353948.2:c.4884T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353949.2:c.4851T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353950.2:c.4851T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353951.2:c.4851T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353952.2:c.4851T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353954.2:c.4848T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353955.2:c.4848T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353957.2:c.4800T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353958.2:c.4800T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353960.2:c.4797T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353961.2:c.2442T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_006920.6:c.4851T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Generalized epilepsy with febrile seizures plus, type 2 (GEFSP2)
Synonyms:: GEFS+, TYPE 2
Identifiers:: MONDO: MONDO:0011461; MedGen: C1858673; Orphanet: 36387; OMIM: 604403

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002820136	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV002820136

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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	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 Neuberg Centre For Genomic Medicine, NCGM, SCV002820136.1

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

Description

This variant has not been reported in affected individuals. The nucleotide change in SCN1A is predicted as conserved by PhyloP across 100 vertebrates. The variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The variant is a loss of function variant but since it is present in the last exon, functional studies will be required to prove protein truncation. Hence this variant has been classified as Uncertain Significance.

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

Last Updated: Apr 6, 2024

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