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NM_001330260.2(SCN8A):c.4879A>C (p.Ile1627Leu) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 3, 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:
RCV000493207.1

Allele description [Variation Report for NM_001330260.2(SCN8A):c.4879A>C (p.Ile1627Leu)]

NM_001330260.2(SCN8A):c.4879A>C (p.Ile1627Leu)

Gene:
SCN8A:sodium voltage-gated channel alpha subunit 8 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.13
Genomic location:
Preferred name:
NM_001330260.2(SCN8A):c.4879A>C (p.Ile1627Leu)
HGVS:
  • NC_000012.12:g.51806365A>C
  • NG_021180.3:g.221408A>C
  • NM_001177984.3:c.4756A>C
  • NM_001330260.2:c.4879A>CMANE SELECT
  • NM_001369788.1:c.4756A>C
  • NM_014191.4:c.4879A>C
  • NP_001171455.1:p.Ile1586Leu
  • NP_001317189.1:p.Ile1627Leu
  • NP_001356717.1:p.Ile1586Leu
  • NP_055006.1:p.Ile1627Leu
  • LRG_1389t1:c.4879A>C
  • LRG_1389t2:c.4879A>C
  • LRG_1389:g.221408A>C
  • LRG_1389p1:p.Ile1627Leu
  • LRG_1389p2:p.Ile1627Leu
  • NC_000012.11:g.52200149A>C
  • NM_014191.3:c.4879A>C
Protein change:
I1586L
Links:
dbSNP: rs1131691414
NCBI 1000 Genomes Browser:
rs1131691414
Molecular consequence:
  • NM_001177984.3:c.4756A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330260.2:c.4879A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369788.1:c.4756A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014191.4:c.4879A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000582082GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(May 3, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000582082.4

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

Description

A variant that is likely pathogenic has been identified in the SCN8A gene. The I1627L variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The I1627L variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution alters a conserved residue predicted to be within the transmembrane segment S4 voltage sensor of the fourth homologous domain. However, the I1627L variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

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

Last Updated: Sep 17, 2022