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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs1057516398

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:23332691 (GRCh38.p14) 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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
SACS : Stop Gained
Publications
1 citation
Genomic View
See rs on genome
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

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.p14 chr 13 NC_000013.11:g.23332691G>A
GRCh37.p13 chr 13 NC_000013.10:g.23906830G>A
SACS RefSeqGene NG_012342.1:g.106012C>T
Gene: SACS, sacsin molecular chaperone (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SACS transcript variant 1 NM_014363.6:c.11185C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform 1 NP_055178.3:p.Gln3729Ter Q (Gln) > * (Ter) Stop Gained
SACS transcript variant 2 NM_001278055.2:c.10744C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform 2 NP_001264984.1:p.Gln3582T…

NP_001264984.1:p.Gln3582Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X1 XM_047430254.1:c.11236C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X1 XP_047286210.1:p.Gln3746T…

XP_047286210.1:p.Gln3746Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X2 XM_005266338.3:c.11212C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X2 XP_005266395.1:p.Gln3738T…

XP_005266395.1:p.Gln3738Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X3 XM_024449337.2:c.11212C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X2 XP_024305105.1:p.Gln3738T…

XP_024305105.1:p.Gln3738Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X4 XM_047430255.1:c.11209C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X3 XP_047286211.1:p.Gln3737T…

XP_047286211.1:p.Gln3737Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X5 XM_011535039.3:c.11203C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X4 XP_011533341.1:p.Gln3735T…

XP_011533341.1:p.Gln3735Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X6 XM_047430256.1:c.11185C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X5 XP_047286212.1:p.Gln3729T…

XP_047286212.1:p.Gln3729Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X7 XM_017020539.2:c.11176C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X6 XP_016876028.1:p.Gln3726T…

XP_016876028.1:p.Gln3726Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X8 XM_047430257.1:c.11065C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X7 XP_047286213.1:p.Gln3689T…

XP_047286213.1:p.Gln3689Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X9 XM_047430258.1:c.11065C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X7 XP_047286214.1:p.Gln3689T…

XP_047286214.1:p.Gln3689Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X10 XM_047430259.1:c.11062C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X8 XP_047286215.1:p.Gln3688T…

XP_047286215.1:p.Gln3688Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X11 XM_047430260.1:c.11056C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X9 XP_047286216.1:p.Gln3686T…

XP_047286216.1:p.Gln3686Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X12 XM_047430261.1:c.11038C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X10 XP_047286217.1:p.Gln3680T…

XP_047286217.1:p.Gln3680Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X13 XM_047430262.1:c.11038C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X10 XP_047286218.1:p.Gln3680T…

XP_047286218.1:p.Gln3680Ter

Q (Gln) > * (Ter) Stop Gained
SACS transcript variant X14 XM_047430263.1:c.11029C>T Q [CAG] > * [TAG] Coding Sequence Variant
sacsin isoform X11 XP_047286219.1:p.Gln3677T…

XP_047286219.1:p.Gln3677Ter

Q (Gln) > * (Ter) Stop Gained
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: A (allele ID: 358143 )
ClinVar Accession Disease Names Clinical Significance
RCV000409109.1 Charlevoix-Saguenay spastic ataxia Likely-Pathogenic
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 G= A
GRCh38.p14 chr 13 NC_000013.11:g.23332691= NC_000013.11:g.23332691G>A
GRCh37.p13 chr 13 NC_000013.10:g.23906830= NC_000013.10:g.23906830G>A
SACS RefSeqGene NG_012342.1:g.106012= NG_012342.1:g.106012C>T
SACS transcript variant 1 NM_014363.6:c.11185= NM_014363.6:c.11185C>T
SACS transcript variant 1 NM_014363.5:c.11185= NM_014363.5:c.11185C>T
SACS transcript variant 2 NM_001278055.2:c.10744= NM_001278055.2:c.10744C>T
SACS transcript variant 2 NM_001278055.1:c.10744= NM_001278055.1:c.10744C>T
SACS transcript variant X2 XM_005266338.3:c.11212= XM_005266338.3:c.11212C>T
SACS transcript variant X1 XM_005266338.2:c.11212= XM_005266338.2:c.11212C>T
SACS transcript variant X2 XM_005266338.1:c.11212= XM_005266338.1:c.11212C>T
SACS transcript variant X5 XM_011535039.3:c.11203= XM_011535039.3:c.11203C>T
SACS transcript variant X3 XM_011535039.2:c.11203= XM_011535039.2:c.11203C>T
SACS transcript variant X3 XM_011535039.1:c.11203= XM_011535039.1:c.11203C>T
SACS transcript variant X3 XM_024449337.2:c.11212= XM_024449337.2:c.11212C>T
SACS transcript variant X2 XM_024449337.1:c.11212= XM_024449337.1:c.11212C>T
SACS transcript variant X7 XM_017020539.2:c.11176= XM_017020539.2:c.11176C>T
SACS transcript variant X4 XM_017020539.1:c.11176= XM_017020539.1:c.11176C>T
SACS transcript variant X6 XM_047430256.1:c.11185= XM_047430256.1:c.11185C>T
SACS transcript variant X9 XM_047430258.1:c.11065= XM_047430258.1:c.11065C>T
SACS transcript variant X13 XM_047430262.1:c.11038= XM_047430262.1:c.11038C>T
SACS transcript variant X8 XM_047430257.1:c.11065= XM_047430257.1:c.11065C>T
SACS transcript variant X12 XM_047430261.1:c.11038= XM_047430261.1:c.11038C>T
SACS transcript variant X1 XM_047430254.1:c.11236= XM_047430254.1:c.11236C>T
SACS transcript variant X4 XM_047430255.1:c.11209= XM_047430255.1:c.11209C>T
SACS transcript variant X11 XM_047430260.1:c.11056= XM_047430260.1:c.11056C>T
SACS transcript variant X14 XM_047430263.1:c.11029= XM_047430263.1:c.11029C>T
SACS transcript variant X10 XM_047430259.1:c.11062= XM_047430259.1:c.11062C>T
sacsin isoform 1 NP_055178.3:p.Gln3729= NP_055178.3:p.Gln3729Ter
sacsin isoform 2 NP_001264984.1:p.Gln3582= NP_001264984.1:p.Gln3582Ter
sacsin isoform X2 XP_005266395.1:p.Gln3738= XP_005266395.1:p.Gln3738Ter
sacsin isoform X4 XP_011533341.1:p.Gln3735= XP_011533341.1:p.Gln3735Ter
sacsin isoform X2 XP_024305105.1:p.Gln3738= XP_024305105.1:p.Gln3738Ter
sacsin isoform X6 XP_016876028.1:p.Gln3726= XP_016876028.1:p.Gln3726Ter
sacsin isoform X5 XP_047286212.1:p.Gln3729= XP_047286212.1:p.Gln3729Ter
sacsin isoform X7 XP_047286214.1:p.Gln3689= XP_047286214.1:p.Gln3689Ter
sacsin isoform X10 XP_047286218.1:p.Gln3680= XP_047286218.1:p.Gln3680Ter
sacsin isoform X7 XP_047286213.1:p.Gln3689= XP_047286213.1:p.Gln3689Ter
sacsin isoform X10 XP_047286217.1:p.Gln3680= XP_047286217.1:p.Gln3680Ter
sacsin isoform X1 XP_047286210.1:p.Gln3746= XP_047286210.1:p.Gln3746Ter
sacsin isoform X3 XP_047286211.1:p.Gln3737= XP_047286211.1:p.Gln3737Ter
sacsin isoform X9 XP_047286216.1:p.Gln3686= XP_047286216.1:p.Gln3686Ter
sacsin isoform X11 XP_047286219.1:p.Gln3677= XP_047286219.1:p.Gln3677Ter
sacsin isoform X8 XP_047286215.1:p.Gln3688= XP_047286215.1:p.Gln3688Ter
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, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss2137338395 Jan 09, 2017 (149)
2 ClinVar RCV000409109.1 Oct 12, 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
RCV000409109.1, ss2137338395 NC_000013.11:23332690:G:A NC_000013.11:23332690:G:A (self)
Help

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

1 citation for rs1057516398
PMID Title Author Year Journal
18604465 A novel mutation in the SACS gene associated with a complicated form of spastic ataxia. Masciullo M et al. 2008 Journal of neurology
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post761+d5e8e07