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NM_001365536.1(SCN9A):c.1997A>G (p.Lys666Arg) AND Generalized epilepsy with febrile seizures plus, type 7

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Dec 18, 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:
RCV000006739.19

Allele description [Variation Report for NM_001365536.1(SCN9A):c.1997A>G (p.Lys666Arg)]

NM_001365536.1(SCN9A):c.1997A>G (p.Lys666Arg)

Genes:
SCN1A-AS1:SCN1A and SCN9A antisense RNA 1 [Gene - HGNC]
SCN9A:sodium voltage-gated channel alpha subunit 9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001365536.1(SCN9A):c.1997A>G (p.Lys666Arg)
Other names:
K655R
HGVS:
  • NC_000002.12:g.166281786T>C
  • NG_012798.1:g.99202A>G
  • NM_001365536.1:c.1997A>GMANE SELECT
  • NM_002977.4:c.1964A>G
  • NP_001352465.1:p.Lys666Arg
  • NP_002968.1:p.Lys655Arg
  • NP_002968.1:p.Lys655Arg
  • NP_002968.2:p.Lys655Arg
  • LRG_369t1:c.1964A>G
  • LRG_369:g.99202A>G
  • LRG_369p1:p.Lys655Arg
  • NC_000002.11:g.167138296T>C
  • NM_002977.2:c.1964A>G
  • NM_002977.3:c.1964A>G
Protein change:
K666R; LYS655ARG
Links:
OMIM: 603415.0019; dbSNP: rs121908919
NCBI 1000 Genomes Browser:
rs121908919
Molecular consequence:
  • NM_001365536.1:c.1997A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002977.4:c.1964A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Generalized epilepsy with febrile seizures plus, type 7 (GEFSP7)
Synonyms:
GEFS+, TYPE 7
Identifiers:
MONDO: MONDO:0013470; MedGen: C2751778; Orphanet: 36387; OMIM: 613863

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000026930OMIM
no assertion criteria provided
Uncertain significance
(Sep 1, 2009)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000746815Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Dec 18, 2017)
inheritedclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

No association between SCN9A and monogenic human epilepsy disorders.

Fasham J, Leslie JS, Harrison JW, Deline J, Williams KB, Kuhl A, Scott Schwoerer J, Cross HE, Crosby AH, Baple EL.

PLoS Genet. 2020 Nov;16(11):e1009161. doi: 10.1371/journal.pgen.1009161.

PubMed [citation]
PMID:
33216760
PMCID:
PMC7717534

A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

Singh NA, Pappas C, Dahle EJ, Claes LR, Pruess TH, De Jonghe P, Thompson J, Dixon M, Gurnett C, Peiffer A, White HS, Filloux F, Leppert MF.

PLoS Genet. 2009 Sep;5(9):e1000649. doi: 10.1371/journal.pgen.1000649. Epub 2009 Sep 18.

PubMed [citation]
PMID:
19763161
PMCID:
PMC2730533
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000026930.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

This variant, previously titled GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 7, has been reclassified based on the report by Fasham et al. (2020), which noted that the K655R variant has a high frequency (0.2%) and is present in homozygous state in the gnomAD database, inconsistent with it being causative of a monogenic seizure disorder.

In a patient with a phenotype consistent with GEFS+, Singh et al. (2009) identified a heterozygous 1964A-G transition in the SCN9A gene, resulting in a lys655-to-arg (K655R) substitution in a highly conserved residue in the large intracellular loop between domains I and II. The mutation was not identified in 562 control chromosomes. The patient had febrile seizures, idiopathic generalized epilepsy, and generalized spike-wave patterns on EEG. Singh et al. (2009) found this mutation in 2 patients diagnosed with Dravet syndrome (607208), one of whom also had a mutation in the SCN1A gene (182389). Singh et al. (2009) suggested that SCN9A mutations may have a modifier effect in partner with SCN1A mutations.

In 2 sisters from a nonconsanguineous Brazilian family with GEFS+, Alves et al. (2019) identified the K655R mutation in the SCN9A gene. The mutation, which was found by whole-exome sequencing, was also present in their unaffected father.

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

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000746815.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 20, 2024