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NM_020822.3(KCNT1):c.1077_1078del (p.Gly361fs)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Feb 12, 2020
Accession:
VCV000289274.5
Variation ID:
289274
Description:
2bp deletion
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NM_020822.3(KCNT1):c.1077_1078del (p.Gly361fs)

Allele ID
273511
Variant type
Deletion
Variant length
2 bp
Cytogenetic location
9q34.3
Genomic location
9: 135765072-135765073 (GRCh38) GRCh38 UCSC
9: 138656918-138656919 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.12:g.135765072_135765073del
NC_000009.11:g.138656918_138656919del
NM_020822.3:c.1077_1078del MANE Select NP_065873.2:p.Gly361fs frameshift
... more HGVS
Protein change
G361fs, G316fs
Other names
-
Canonical SPDI
NC_000009.12:135765071:AG:
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00007
Exome Aggregation Consortium (ExAC) 0.00004
Links
ClinGen: CA5326765
dbSNP: rs796214553
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts May 11, 2017 RCV000726307.4
Likely benign 1 criteria provided, single submitter Feb 12, 2020 RCV001081547.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNT1 - - GRCh38
GRCh37
1216 1274

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 11, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000582313.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
A variant of uncertain significance has been identified in the KCNT1 gene. The c.1077_1078delAG variant has not been published as a pathogenic variant, nor has … (more)
Likely benign
(Feb 12, 2020)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, 5
Early infantile epileptic encephalopathy 14
Allele origin: germline
Invitae
Accession: SCV000834343.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Aug 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000343609.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KCNT1 - - - -

Text-mined citations for rs796214553...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 06, 2021