NM_001165963.4(SCN1A):c.4999del (p.Leu1667fs) AND Generalized epilepsy with febrile seizures plus, type 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 22, 2021
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:: RCV001580609.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.4999del (p.Leu1667fs)]

NM_001165963.4(SCN1A):c.4999del (p.Leu1667fs)

Genes:

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

Variant type:

Deletion

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.4999del (p.Leu1667fs)

HGVS:

NC_000002.12:g.165992278del
NG_011906.1:g.86364del
NM_001165963.4:c.4999delMANE SELECT
NM_001165964.3:c.4915del
NM_001202435.3:c.4999del
NM_001353948.2:c.4999del
NM_001353949.2:c.4966del
NM_001353950.2:c.4966del
NM_001353951.2:c.4966del
NM_001353952.2:c.4966del
NM_001353954.2:c.4963del
NM_001353955.2:c.4963del
NM_001353957.2:c.4915del
NM_001353958.2:c.4915del
NM_001353960.2:c.4912del
NM_001353961.2:c.2557del
NM_006920.6:c.4966del
NP_001159435.1:p.Leu1667fs
NP_001159436.1:p.Leu1639fs
NP_001189364.1:p.Leu1667fs
NP_001340877.1:p.Leu1667fs
NP_001340878.1:p.Leu1656fs
NP_001340879.1:p.Leu1656fs
NP_001340880.1:p.Leu1656fs
NP_001340881.1:p.Leu1656fs
NP_001340883.1:p.Leu1655fs
NP_001340884.1:p.Leu1655fs
NP_001340886.1:p.Leu1639fs
NP_001340887.1:p.Leu1639fs
NP_001340889.1:p.Leu1638fs
NP_001340890.1:p.Leu853fs
NP_008851.3:p.Leu1656fs
LRG_8:g.86364del
NC_000002.11:g.166848788del
NM_001165963.2:c.4999delC
NR_148667.2:n.5416del

Protein change:

L1638fs

Links:

dbSNP: rs2105433855

NCBI 1000 Genomes Browser:

rs2105433855

Molecular consequence:

NM_001165963.4:c.4999del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165964.3:c.4915del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001202435.3:c.4999del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353948.2:c.4999del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353949.2:c.4966del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353950.2:c.4966del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353951.2:c.4966del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353952.2:c.4966del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353954.2:c.4963del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353955.2:c.4963del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353957.2:c.4915del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353958.2:c.4915del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353960.2:c.4912del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001353961.2:c.2557del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006920.6:c.4966del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148667.2:n.5416del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001810217	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 22, 2021)	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

SCV001810217

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 22, 2021)

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 Genome-Nilou Lab, SCV001810217.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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