NM_001165963.4(SCN1A):c.4786C>T (p.Arg1596Cys) AND Generalized epilepsy with febrile seizures plus, type 2

Clinical significance:Likely pathogenic (Last evaluated: Dec 11, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001031013.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.4786C>T (p.Arg1596Cys)]

NM_001165963.4(SCN1A):c.4786C>T (p.Arg1596Cys)

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.4786C>T (p.Arg1596Cys)
Other names:
p.R1596C:CGC>TGC
HGVS:
  • NC_000002.12:g.165994212G>A
  • NG_011906.1:g.84428C>T
  • NM_001165963.4:c.4786C>TMANE SELECT
  • NM_001165963.4:c.4786C>T
  • NM_001165964.3:c.4702C>T
  • NM_001202435.3:c.4786C>T
  • NM_001353948.2:c.4786C>T
  • NM_001353949.2:c.4753C>T
  • NM_001353950.2:c.4753C>T
  • NM_001353951.2:c.4753C>T
  • NM_001353952.2:c.4753C>T
  • NM_001353954.2:c.4750C>T
  • NM_001353955.2:c.4750C>T
  • NM_001353957.2:c.4702C>T
  • NM_001353958.2:c.4702C>T
  • NM_001353960.2:c.4699C>T
  • NM_001353961.2:c.2344C>T
  • NM_006920.6:c.4753C>T
  • NP_001159435.1:p.Arg1596Cys
  • NP_001159436.1:p.Arg1568Cys
  • NP_001189364.1:p.Arg1596Cys
  • NP_001340877.1:p.Arg1596Cys
  • NP_001340878.1:p.Arg1585Cys
  • NP_001340879.1:p.Arg1585Cys
  • NP_001340880.1:p.Arg1585Cys
  • NP_001340881.1:p.Arg1585Cys
  • NP_001340883.1:p.Arg1584Cys
  • NP_001340884.1:p.Arg1584Cys
  • NP_001340886.1:p.Arg1568Cys
  • NP_001340887.1:p.Arg1568Cys
  • NP_001340889.1:p.Arg1567Cys
  • NP_001340890.1:p.Arg782Cys
  • NP_008851.3:p.Arg1585Cys
  • LRG_8t1:c.4753C>T
  • LRG_8:g.84428C>T
  • NC_000002.11:g.166850722G>A
  • NM_001165963.1:c.4786C>T
  • NM_006920.4:c.4753C>T
  • NR_148667.2:n.5203C>T
  • p.R1585C
Protein change:
R1567C
Links:
UniProtKB/Swiss-Prot: VAR_043368; dbSNP: rs121917993
NCBI 1000 Genomes Browser:
rs121917993
Molecular consequence:
  • NM_001165963.4:c.4786C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.4702C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.4786C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.4786C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.4753C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.4753C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.4753C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.4753C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.4750C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.4750C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.4702C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.4702C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.4699C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.2344C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.4753C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.5203C>T - 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001160806Cavalleri Lab, Royal College of Surgeons in Irelandcriteria provided, single submitter
Likely pathogenic
(Dec 11, 2019)
de novoresearch

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyesnot providednot providednot providednot providednot providedresearch

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

A comparison of genomic diagnostics in adults and children with epilepsy and comorbid intellectual disability.

Benson KA, White M, Allen NM, Byrne S, Carton R, Comerford E, Costello D, Doherty C, Dunleavey B, El-Naggar H, Gangadharan N, Heavin S, Kearney H, Lench NJ, Lynch J, McCormack M, Regan MO, Podesta K, Power K, Rogers AS, Steward CA, Sweeney B, et al.

Eur J Hum Genet. 2020 Aug;28(8):1066-1077. doi: 10.1038/s41431-020-0610-3. Epub 2020 Apr 1.

PubMed [citation]
PMID:
32238909
PMCID:
PMC7381648

Details of each submission

From Cavalleri Lab, Royal College of Surgeons in Ireland, SCV001160806.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)

Description

ACMG evidence PS2, PP2, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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