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NM_001165963.4(SCN1A):c.5066T>C (p.Met1689Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1); Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3
First in ClinVar:
May 13, 2019
Most recent Submission:
May 16, 2022
Last evaluated:
Sep 1, 2021
Accession:
VCV000627412.8
Variation ID:
627412
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.5066T>C (p.Met1689Thr)

Allele ID
615767
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165992209 (GRCh38) GRCh38 UCSC
2: 166848719 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001165963.4:c.5066T>C MANE Select NP_001159435.1:p.Met1689Thr missense
NM_001165964.3:c.4982T>C NP_001159436.1:p.Met1661Thr missense
NM_001202435.3:c.5066T>C NP_001189364.1:p.Met1689Thr missense
... more HGVS
Protein change
M1678T, M1689T, M1661T, M1660T, M875T, M1677T
Other names
-
Canonical SPDI
NC_000002.12:165992208:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter May 3, 2019 RCV000770782.2
Uncertain significance 1 criteria provided, single submitter Apr 4, 2018 RCV001004769.2
Uncertain significance 1 criteria provided, single submitter Sep 1, 2021 RCV001216747.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SCN1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1646 3367
LOC102724058 - - - GRCh38 - 1673

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Likely pathogenic
(May 03, 2019)
criteria provided, single submitter
Method: clinical testing
Generalized epilepsy with febrile seizures plus, type 2
(Autosomal dominant inheritance)
Affected status: yes
Allele origin: maternal
Génétique des Maladies du Développement, Hospices Civils de Lyon
Accession: SCV000902247.1
First in ClinVar: May 13, 2019
Last updated: May 13, 2019
Comment:
Familial segregation
Zygosity: 1 Single Heterozygote
Sex: male
Uncertain significance
(Apr 04, 2018)
criteria provided, single submitter
Method: clinical testing
Severe myoclonic epilepsy in infancy
(Autosomal dominant inheritance)
Affected status: yes
Allele origin: paternal
Génétique des Maladies du Développement, Hospices Civils de Lyon
Accession: SCV001164249.1
First in ClinVar: Mar 01, 2020
Last updated: Mar 01, 2020
Uncertain significance
(Sep 01, 2021)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001388559.3
First in ClinVar: Jul 16, 2020
Last updated: May 16, 2022

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Record last updated Aug 24, 2022