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dbSNP Short Genetic Variations

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs121918733

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr2:166058684 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
SCN1A : Missense Variant
Publications
4 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 2 NC_000002.12:g.166058684A>G
GRCh37.p13 chr 2 NC_000002.11:g.166915194A>G
SCN1A RefSeqGene (LRG_8) NG_011906.1:g.19956T>C
Gene: SCN1A, sodium voltage-gated channel alpha subunit 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SCN1A transcript variant 15 NM_001353961.1:c. N/A 5 Prime UTR Variant
SCN1A transcript variant 1 NM_001165963.2:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 1 NP_001159435.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 2 NM_006920.5:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 2 NP_008851.3:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 3 NM_001165964.2:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 3 NP_001159436.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 5 NM_001353948.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 1 NP_001340877.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 4 NM_001202435.2:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 1 NP_001189364.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 6 NM_001353949.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 2 NP_001340878.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 7 NM_001353950.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 2 NP_001340879.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 8 NM_001353951.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 2 NP_001340880.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 9 NM_001353952.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 2 NP_001340881.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 10 NM_001353954.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 4 NP_001340883.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 11 NM_001353955.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 4 NP_001340884.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 12 NM_001353957.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 3 NP_001340886.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 13 NM_001353958.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 3 NP_001340887.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 14 NM_001353960.1:c.269T>C F [TTT] > S [TCT] Coding Sequence Variant
sodium channel protein type 1 subunit alpha isoform 5 NP_001340889.1:p.Phe90Ser F (Phe) > S (Ser) Missense Variant
SCN1A transcript variant 16 NR_148667.1:n.674T>C N/A Non Coding Transcript Variant
SCN1A transcript variant X1 XR_001738883.1:n.655T>C N/A Non Coding Transcript Variant
SCN1A transcript variant X2 XR_001738884.1:n.660T>C N/A Non Coding Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: G (allele ID: 79488 )
ClinVar Accession Disease Names Clinical Significance
RCV000059473.4 Severe myoclonic epilepsy in infancy Pathogenic-Likely-Pathogenic
RCV000332135.1 Generalized epilepsy with febrile seizures plus, type 2 Likely-Pathogenic
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

None
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement A= G Note
GRCh38.p12 chr 2 NC_000002.12:g.166058684A= NC_000002.12:g.16605868...

NC_000002.12:g.166058684A>G

GRCh37.p13 chr 2 NC_000002.11:g.166915194A= NC_000002.11:g.16691519...

NC_000002.11:g.166915194A>G

SCN1A RefSeqGene (LRG_8) NG_011906.1:g.19956T= NG_011906.1:g.19956T>C
SCN1A transcript variant 2 NM_006920.5:c.269T= NM_006920.5:c.269T>C
SCN1A transcript variant 2 NM_006920.4:c.269T= NM_006920.4:c.269T>C
SCN1A transcript variant 4 NM_001202435.2:c.269T= NM_001202435.2:c.269T>C
SCN1A transcript variant 4 NM_001202435.1:c.269T= NM_001202435.1:c.269T>C
SCN1A transcript variant 1 NM_001165963.2:c.269T= NM_001165963.2:c.269T>C
SCN1A transcript variant 1 NM_001165963.1:c.269T= NM_001165963.1:c.269T>C
SCN1A transcript variant 3 NM_001165964.2:c.269T= NM_001165964.2:c.269T>C
SCN1A transcript variant 3 NM_001165964.1:c.269T= NM_001165964.1:c.269T>C
SCN1A transcript variant 15 NM_001353961.1:c.-2157T= NM_001353961.1:c.-2157T>C
SCN1A transcript variant 7 NM_001353950.1:c.269T= NM_001353950.1:c.269T>C
SCN1A transcript variant 9 NM_001353952.1:c.269T= NM_001353952.1:c.269T>C
SCN1A transcript variant 10 NM_001353954.1:c.269T= NM_001353954.1:c.269T>C
SCN1A transcript variant 16 NR_148667.1:n.674T= NR_148667.1:n.674T>C
SCN1A transcript variant 13 NM_001353958.1:c.269T= NM_001353958.1:c.269T>C
SCN1A transcript variant 5 NM_001353948.1:c.269T= NM_001353948.1:c.269T>C
SCN1A transcript variant 14 NM_001353960.1:c.269T= NM_001353960.1:c.269T>C
SCN1A transcript variant 8 NM_001353951.1:c.269T= NM_001353951.1:c.269T>C
SCN1A transcript variant 11 NM_001353955.1:c.269T= NM_001353955.1:c.269T>C
SCN1A transcript variant 6 NM_001353949.1:c.269T= NM_001353949.1:c.269T>C
SCN1A transcript variant 12 NM_001353957.1:c.269T= NM_001353957.1:c.269T>C
SCN1A transcript variant X1 XR_001738883.1:n.655T= XR_001738883.1:n.655T>C
SCN1A transcript variant X2 XR_001738884.1:n.660T= XR_001738884.1:n.660T>C
sodium channel protein type 1 subunit alpha isoform 2 NP_008851.3:p.Phe90= NP_008851.3:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 1 NP_001189364.1:p.Phe90= NP_001189364.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 1 NP_001159435.1:p.Phe90= NP_001159435.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 3 NP_001159436.1:p.Phe90= NP_001159436.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 2 NP_001340879.1:p.Phe90= NP_001340879.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 2 NP_001340881.1:p.Phe90= NP_001340881.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 4 NP_001340883.1:p.Phe90= NP_001340883.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 3 NP_001340887.1:p.Phe90= NP_001340887.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 1 NP_001340877.1:p.Phe90= NP_001340877.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 5 NP_001340889.1:p.Phe90= NP_001340889.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 2 NP_001340880.1:p.Phe90= NP_001340880.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 4 NP_001340884.1:p.Phe90= NP_001340884.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 2 NP_001340878.1:p.Phe90= NP_001340878.1:p.Phe90Ser
sodium channel protein type 1 subunit alpha isoform 3 NP_001340886.1:p.Phe90= NP_001340886.1:p.Phe90Ser
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

1 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SWISSPROT ss275523593 Dec 10, 2010 (133)
2 ClinVar RCV000059473.4 Oct 11, 2018 (152)
3 ClinVar RCV000332135.1 Oct 11, 2018 (152)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss275523593 NC_000002.12:166058683:A= NC_000002.12:166058683:A= (self)
RCV000059473.4, RCV000332135.1, ss275523593 NC_000002.12:166058683:A>G NC_000002.12:166058683:A>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs121918733
PMID Title Author Year Journal
18554359 Seven novel SCN1A mutations in Chinese patients with severe myoclonic epilepsy of infancy. Sun H et al. 2008 Epilepsia
20431604 Analysis of SCN1A mutation and parental origin in patients with Dravet syndrome. Sun H et al. 2010 Journal of human genetics
23195492 Prevalence of SCN1A mutations in children with suspected Dravet syndrome and intractable childhood epilepsy. Wang JW et al. 2012 Epilepsy research
26096185 Amplicon Resequencing Identified Parental Mosaicism for Approximately 10% of "de novo" SCN1A Mutations in Children with Dravet Syndrome. Xu X et al. 2015 Human mutation

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post58+e54ea20