NM_020822.3(KCNT1):c.2280C>G (p.Ile760Met) AND not provided

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Mar 1, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000413294.4

Allele description [Variation Report for NM_020822.3(KCNT1):c.2280C>G (p.Ile760Met)]

NM_020822.3(KCNT1):c.2280C>G (p.Ile760Met)

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.2280C>G (p.Ile760Met)
HGVS:
  • NC_000009.12:g.135775346C>G
  • NG_033070.1:g.78162C>G
  • NM_001272003.2:c.2145C>G
  • NM_020822.3:c.2280C>GMANE SELECT
  • NP_001258932.1:p.Ile715Met
  • NP_065873.2:p.Ile760Met
  • NC_000009.11:g.138667192C>G
  • NM_020822.2:c.2280C>G
Protein change:
I715M; ILE760MET
Links:
OMIM: 608167.0004; dbSNP: rs370521183
NCBI 1000 Genomes Browser:
rs370521183
Molecular consequence:
  • NM_001272003.2:c.2145C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020822.3:c.2280C>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
4

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000491097GeneDxcriteria provided, single submitter
Likely pathogenic
(Oct 5, 2015)
germlineclinical testing

Citation Link,

SCV001247126CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Pathogenic
(Mar 1, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes4not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000491097.2

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

Description

The I760M variant in the KCNT1 gene has been previously reported in a female with malignantmigrating partial seizures of infancy (Barcia et al., 2012). The I760M variant was not observed inapproximately 6500 individuals of European and African American ancestry in the NHLBI ExomeSequencing Project, indicating it is not a common benign variant in these populations. The I760Mvariant is a conservative amino acid substitution, which occurs at a position that is conserved acrossspecies. In silico analysis predicts this variant is probably damaging to the protein structure/function. The I760M variant is a strong candidate for a pathogenic variant.

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001247126.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided4not providednot providednot provided

Last Updated: Oct 6, 2021

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