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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs121434379

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr9:132296909 (GRCh38.p7) 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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00002 (4/246242, GnomAD)
C=0.00002 (2/125568, TOPMED)
C=0.00001 (1/121400, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SETX : Missense Variant
Publications
2 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.p7 chr 9 NC_000009.12:g.132296909A>C
GRCh37.p13 chr 9 NC_000009.11:g.135172296A>C
SETX RefSeqGene (LRG_268) NG_007946.1:g.63077T>G
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: C (allele ID: 17331 )
ClinVar Accession Disease Names Clinical Significance
RCV000002382.5 Spinocerebellar ataxia autosomal recessive 1 Pathogenic
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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").

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Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 246242 A=0.99998 C=0.00002
The Genome Aggregation Database European Sub 133998 A=0.99997 C=0.00003
The Genome Aggregation Database Asian Sub 48024 A=1.0000 C=0.0000
The Genome Aggregation Database American Sub 33582 A=1.0000 C=0.0000
The Genome Aggregation Database African Sub 15304 A=1.0000 C=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 A=1.000 C=0.000
The Genome Aggregation Database Other Sub 5484 A=1.000 C=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.99998 C=0.00002
The Exome Aggregation Consortium Global Study-wide 121400 A=0.99999 C=0.00001
The Exome Aggregation Consortium Europe Sub 73348 A=1.0000 C=0.0000
The Exome Aggregation Consortium Asian Sub 25162 A=1.0000 C=0.0000
The Exome Aggregation Consortium American Sub 11576 A=1.0000 C=0.0000
The Exome Aggregation Consortium African Sub 10406 A=1.0000 C=0.0000
The Exome Aggregation Consortium Other Sub 908 A=1.00 C=0.00
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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= C Note
GRCh38.p7 chr 9 NC_000009.12:g.132296909A= NC_000009.12:g.13229690...

NC_000009.12:g.132296909A>C

GRCh37.p13 chr 9 NC_000009.11:g.135172296A= NC_000009.11:g.13517229...

NC_000009.11:g.135172296A>C

SETX RefSeqGene (LRG_268) NG_007946.1:g.63077T= NG_007946.1:g.63077T>G
SETX transcript NM_015046.5:c.5927T= NM_015046.5:c.5927T>G
SETX transcript variant X8 XR_929739.2:n.5843T= XR_929739.2:n.5843T>G
SETX transcript variant X5 XM_011518405.2:c.5927T= XM_011518405.2:c.5927T>G
SETX transcript variant X4 XM_011518404.2:c.5927T= XM_011518404.2:c.5927T>G
SETX transcript variant X3 XM_005272173.2:c.5927T= XM_005272173.2:c.5927T>G
SETX transcript variant X4 XM_005272173.1:c.5927T= XM_005272173.1:c.5927T>G
SETX transcript variant X2 XM_005272172.2:c.5927T= XM_005272172.2:c.5927T>G
SETX transcript variant X2 XM_005272172.1:c.5927T= XM_005272172.1:c.5927T>G
SETX transcript variant X5 XM_011518406.2:c.5927T= XM_011518406.2:c.5927T>G
SETX transcript variant X9 XM_011518408.2:c.5927T= XM_011518408.2:c.5927T>G
SETX transcript variant X1 XM_005272171.1:c.5927T= XM_005272171.1:c.5927T>G
SETX transcript variant X6 XM_017014495.1:c.5927T= XM_017014495.1:c.5927T>G
SETX transcript variant X9 XR_001746251.1:n.5482T= XR_001746251.1:n.5482T>G
SETX transcript variant X6 XM_011518407.1:c.5927T= XM_011518407.1:c.5927T>G
SETX transcript variant X13 XM_017014497.1:c.380T= XM_017014497.1:c.380T>G
SETX transcript variant X10 XM_017014496.1:c.380T= XM_017014496.1:c.380T>G
probable helicase senataxin isoform 1 NP_055861.3:p.Leu1976= NP_055861.3:p.Leu1976Arg
probable helicase senataxin isoform X1 XP_011516707.1:p.Leu1976= XP_011516707.1:p.Leu197...

XP_011516707.1:p.Leu1976Arg

probable helicase senataxin isoform X1 XP_011516706.1:p.Leu1976= XP_011516706.1:p.Leu197...

XP_011516706.1:p.Leu1976Arg

probable helicase senataxin isoform X1 XP_005272230.1:p.Leu1976= XP_005272230.1:p.Leu197...

XP_005272230.1:p.Leu1976Arg

probable helicase senataxin isoform X1 XP_005272229.1:p.Leu1976= XP_005272229.1:p.Leu197...

XP_005272229.1:p.Leu1976Arg

probable helicase senataxin isoform X2 XP_011516708.1:p.Leu1976= XP_011516708.1:p.Leu197...

XP_011516708.1:p.Leu1976Arg

probable helicase senataxin isoform X4 XP_011516710.1:p.Leu1976= XP_011516710.1:p.Leu197...

XP_011516710.1:p.Leu1976Arg

probable helicase senataxin isoform X1 XP_005272228.1:p.Leu1976= XP_005272228.1:p.Leu197...

XP_005272228.1:p.Leu1976Arg

probable helicase senataxin isoform X2 XP_016869984.1:p.Leu1976= XP_016869984.1:p.Leu197...

XP_016869984.1:p.Leu1976Arg

probable helicase senataxin isoform X3 XP_011516709.1:p.Leu1976= XP_011516709.1:p.Leu197...

XP_011516709.1:p.Leu1976Arg

probable helicase senataxin isoform X7 XP_016869986.1:p.Leu127= XP_016869986.1:p.Leu127Arg
probable helicase senataxin isoform X5 XP_016869985.1:p.Leu127= XP_016869985.1:p.Leu127Arg
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#.

3 Frequency, 7 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss256301950 Aug 25, 2010 (132)
2 EVA_EXAC ss1689710926 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2314961813 Dec 20, 2016 (150)
4 GNOMAD ss2737954558 Nov 08, 2017 (151)
5 TOPMED ss3602239764 Nov 08, 2017 (151)
6 ILLUMINA ss3625992876 Jul 20, 2018 (151)
7 ILLUMINA ss3625992877 Jul 20, 2018 (151)
8 The Exome Aggregation Consortium NC_000009.11 - 135172296 Jul 20, 2018 (151)
9 The Genome Aggregation Database NC_000009.11 - 135172296 Jul 20, 2018 (151)
10 Trans-Omics for Precision Medicine NC_000009.12 - 132296909 Jul 20, 2018 (151)
11 ClinVar RCV000002382.5 Jul 20, 2018 (151)
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
9850620, 6969293, ss1689710926, ss2737954558, ss3625992876, ss3625992877 NC_000009.11:135172295:A= NC_000009.12:132296908:A= (self)
421576216, ss256301950, ss2314961813, ss3602239764 NC_000009.12:132296908:A= NC_000009.12:132296908:A= (self)
9850620, 6969293, ss1689710926, ss2737954558, ss3625992876, ss3625992877 NC_000009.11:135172295:A>C NC_000009.12:132296908:A>C (self)
RCV000002382.5, 421576216, ss256301950, ss2314961813, ss3602239764 NC_000009.12:132296908:A>C NC_000009.12:132296908:A>C (self)
Help

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

2 citations for rs121434379
PMID Title Author Year Journal
15732101 Mutations in senataxin responsible for Quebec cluster of ataxia with neuropathy. Duquette A et al. 2005 Annals of neurology
17159128 Novel mutations in the senataxin DNA/RNA helicase domain in ataxia with oculomotor apraxia 2. Fogel BL et al. 2006 Neurology

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: 0.1.4.post863+3a64c51