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NM_001165963.4(SCN1A):c.5726C>T (p.Thr1909Ile)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5
First in ClinVar:
Oct 31, 2013
Most recent Submission:
Aug 23, 2022
Last evaluated:
Aug 12, 2021
Accession:
VCV000068669.16
Variation ID:
68669
Description:
single nucleotide variant
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NM_001165963.4(SCN1A):c.5726C>T (p.Thr1909Ile)

Allele ID
79561
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q24.3
Genomic location
2: 165991549 (GRCh38) GRCh38 UCSC
2: 166848059 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001165963.4:c.5726C>T MANE Select NP_001159435.1:p.Thr1909Ile missense
NM_001165964.3:c.5642C>T NP_001159436.1:p.Thr1881Ile missense
NM_001202435.3:c.5726C>T NP_001189364.1:p.Thr1909Ile missense
... more HGVS
Protein change
T1898I, T1909I, T1897I, T1095I, T1880I, T1881I
Other names
-
Canonical SPDI
NC_000002.12:165991548:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA285249
UniProtKB/Swiss-Prot: VAR_029729
dbSNP: rs121918793
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts May 1, 2018 RCV000494436.9
Pathogenic 2 criteria provided, single submitter Jan 6, 2017 RCV000059549.4
Pathogenic 1 criteria provided, single submitter Aug 12, 2021 RCV000705871.3
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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 3370
LOC102724058 - - - GRCh38 - 1676

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(Jan 06, 2017)
criteria provided, single submitter
Method: clinical testing
Epileptic encephalopathy, early infantile, 6 (Dravet syndrome)
Affected status: yes
Allele origin: de novo
Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris
Accession: SCV000586771.1
First in ClinVar: Aug 05, 2017
Last updated: Aug 05, 2017
Publications:
PubMed (1)
PubMed: 28708303
Comment:
Intellectual disability; severe and pharmacoresistant epilepsy (starting with febrile convulsions); pyramidal syndrome; tremor and myoclonus; dysmorphism; scoliosis
Number of individuals with the variant: 1
Age: 30-39 years
Sex: male
Likely pathogenic
(May 01, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV000581895.3
First in ClinVar: Jul 02, 2017
Last updated: Jul 02, 2017
Comment:
A variant that is likely pathogenic has been identified in the SCN1A gene. The T1909I variant has been previously reported as T1899I (using alternative nomenclature) … (more)
Pathogenic
(Aug 12, 2021)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV000834888.2
First in ClinVar: Oct 10, 2018
Last updated: May 16, 2022
Publications:
PubMed (1)
PubMed: 28492532
Pathogenic
(May 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: yes
Allele origin: germline
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001245858.11
First in ClinVar: May 12, 2020
Last updated: Aug 23, 2022
Number of individuals with the variant: 1
not provided
(-)
no assertion provided
Method: not provided
Severe myoclonic epilepsy in infancy
Affected status: not provided
Allele origin: not provided
UniProtKB/Swiss-Prot
Accession: SCV000091081.1
First in ClinVar: Oct 31, 2013
Last updated: Oct 31, 2013

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
Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients. Chérot E Clinical genetics 2018 PMID: 28708303
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
Significant correlation of the SCN1A mutations and severe myoclonic epilepsy in infancy. Ohmori I Biochemical and biophysical research communications 2002 PMID: 12083760

Text-mined citations for rs121918793...

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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 Aug 24, 2022