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NM_001165963.4(SCN1A):c.5864T>C (p.Ile1955Thr) AND Generalized epilepsy with febrile seizures plus, type 2

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 27, 2017
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:
RCV001133025.12

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5864T>C (p.Ile1955Thr)]

NM_001165963.4(SCN1A):c.5864T>C (p.Ile1955Thr)

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.5864T>C (p.Ile1955Thr)
Other names:
p.I1955T:ATA>ACA
HGVS:
  • NC_000002.12:g.165991411A>G
  • NG_011906.1:g.87229T>C
  • NM_001165963.4:c.5864T>CMANE SELECT
  • NM_001165963.4:c.5864T>C
  • NM_001165964.3:c.5780T>C
  • NM_001202435.3:c.5864T>C
  • NM_001353948.2:c.5864T>C
  • NM_001353949.2:c.5831T>C
  • NM_001353950.2:c.5831T>C
  • NM_001353951.2:c.5831T>C
  • NM_001353952.2:c.5831T>C
  • NM_001353954.2:c.5828T>C
  • NM_001353955.2:c.5828T>C
  • NM_001353957.2:c.5780T>C
  • NM_001353958.2:c.5780T>C
  • NM_001353960.2:c.5777T>C
  • NM_001353961.2:c.3422T>C
  • NM_006920.6:c.5831T>C
  • NP_001159435.1:p.Ile1955Thr
  • NP_001159436.1:p.Ile1927Thr
  • NP_001189364.1:p.Ile1955Thr
  • NP_001340877.1:p.Ile1955Thr
  • NP_001340878.1:p.Ile1944Thr
  • NP_001340879.1:p.Ile1944Thr
  • NP_001340880.1:p.Ile1944Thr
  • NP_001340881.1:p.Ile1944Thr
  • NP_001340883.1:p.Ile1943Thr
  • NP_001340884.1:p.Ile1943Thr
  • NP_001340886.1:p.Ile1927Thr
  • NP_001340887.1:p.Ile1927Thr
  • NP_001340889.1:p.Ile1926Thr
  • NP_001340890.1:p.Ile1141Thr
  • NP_008851.3:p.Ile1944Thr
  • LRG_8:g.87229T>C
  • NC_000002.11:g.166847921A>G
  • NM_001165963.1:c.5864T>C
  • NM_001202435.1:c.5864T>C
  • NR_148667.2:n.6281T>C
  • P35498:p.Ile1955Thr
Protein change:
I1141T
Links:
UniProtKB: P35498#VAR_029730; dbSNP: rs35735053
NCBI 1000 Genomes Browser:
rs35735053
Molecular consequence:
  • NM_001165963.4:c.5864T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5780T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5864T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5864T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5828T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5828T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5780T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5780T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5777T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.3422T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.6281T>C - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001292711Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Apr 27, 2017) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001292711.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024