NM_020822.3(KCNT1):c.3544A>C (p.Ile1182Leu) AND Epilepsy, nocturnal frontal lobe, 5

Clinical significance:Uncertain significance (Last evaluated: Mar 6, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001270712.1

Allele description [Variation Report for NM_020822.3(KCNT1):c.3544A>C (p.Ile1182Leu)]

NM_020822.3(KCNT1):c.3544A>C (p.Ile1182Leu)

Gene:
KCNT1:potassium sodium-activated channel subfamily T member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_020822.3(KCNT1):c.3544A>C (p.Ile1182Leu)
HGVS:
  • NC_000009.12:g.135791838A>C
  • NG_033070.1:g.94654A>C
  • NM_001272003.2:c.3472A>C
  • NM_020822.3:c.3544A>CMANE SELECT
  • NP_001258932.1:p.Ile1158Leu
  • NP_065873.2:p.Ile1182Leu
  • NC_000009.11:g.138683684A>C
  • NM_020822.2:c.3544A>C
Protein change:
I1158L
Links:
Molecular consequence:
  • NM_001272003.2:c.3472A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.3544A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Epilepsy, nocturnal frontal lobe, 5 (ENFL5)
Synonyms:
CILIARY DYSKINESIA, PRIMARY, 28, WITHOUT SITUS INVERSUS; CILIARY DYSKINESIA, PRIMARY, 28, WITH SITUS INVERSUS
Identifiers:
MONDO: MONDO:0014002; MedGen: C3554306; Orphanet: 98784; OMIM: 615005

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001451457Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Mar 6, 2019)
unknownclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV001451457.1

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

Description

The KCNT1 c.3544A>C (p.Ile1182Leu) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found through this search. This variant is reported at a frequency of 0.000009 in the European (non-Finnish) population of the Genome Aggregation Database. This frequency is based on one allele only in a region of good sequencing coverage, so the variant is presumed to be rare. The p.Ile1182Leu variant is not located in a known functional domain, and in silico algorithms differ in their predictions about the consequence of this variant. Missense variants are a known cause of KCNT1-related epilepsy, but considerable benign missense variation in this gene has been reported. Based on the limited evidence available, the p.Ile1182Leu variant is classified as a variant of uncertain significance for KCNT1-related epilepsy.

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

Last Updated: Jun 6, 2021

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