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NM_020822.3(KCNT1):c.885G>A (p.Ala295=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Oct 1, 2021)
Last evaluated:
May 20, 2021
Accession:
VCV000193923.9
Variation ID:
193923
Description:
single nucleotide variant
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NM_020822.3(KCNT1):c.885G>A (p.Ala295=)

Allele ID
191086
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.3
Genomic location
9: 135759709 (GRCh38) GRCh38 UCSC
9: 138651555 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.138651555G>A
NC_000009.12:g.135759709G>A
NG_033070.1:g.62525G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:135759708:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00036
Trans-Omics for Precision Medicine (TOPMed) 0.00056
Trans-Omics for Precision Medicine (TOPMed) 0.00033
The Genome Aggregation Database (gnomAD), exomes 0.00055
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
The Genome Aggregation Database (gnomAD) 0.00032
Exome Aggregation Consortium (ExAC) 0.00065
Links
ClinGen: CA239657
dbSNP: rs142756900
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Feb 23, 2017 RCV000174155.7
Likely benign 1 criteria provided, single submitter Aug 15, 2016 RCV000716669.1
Benign 1 criteria provided, single submitter Dec 2, 2020 RCV001082687.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 20, 2021 RCV000724073.4
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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
1240 1298

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 09, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225403.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Feb 23, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000613896.1
Submitted: (Aug 17, 2017)
Evidence details
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, 5
Early infantile epileptic encephalopathy 14
Allele origin: germline
Invitae
Accession: SCV000652967.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(May 20, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000523094.5
Submitted: (Oct 01, 2021)
Evidence details
Likely benign
(Aug 15, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847511.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign

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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KCNT1 - - - -

Text-mined citations for rs142756900...

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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 Nov 27, 2021