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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 Aliases 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.

rs80338777

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr1:201077915 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00001 (3/251124, GnomAD_exome)
A=0.00003 (4/125568, TOPMED)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CACNA1S : Missense Variant
Publications
6 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 1 NC_000001.11:g.201077915C>A
GRCh38.p12 chr 1 NC_000001.11:g.201077915C>T
GRCh37.p13 chr 1 NC_000001.10:g.201047043C>A
GRCh37.p13 chr 1 NC_000001.10:g.201047043C>T
CACNA1S RefSeqGene NG_009816.2:g.39652G>T
CACNA1S RefSeqGene NG_009816.2:g.39652G>A
CACNA1S RefSeqGene NG_009816.1:g.39652G>T
CACNA1S RefSeqGene NG_009816.1:g.39652G>A
Gene: CACNA1S, calcium voltage-gated channel subunit alpha1 S (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CACNA1S transcript NM_000069.3:c.1583G>T R [CGC] > L [CTC] Coding Sequence Variant
voltage-dependent L-type calcium channel subunit alpha-1S NP_000060.2:p.Arg528Leu R (Arg) > L (Leu) Missense Variant
CACNA1S transcript NM_000069.3:c.1583G>A R [CGC] > H [CAC] Coding Sequence Variant
voltage-dependent L-type calcium channel subunit alpha-1S NP_000060.2:p.Arg528His R (Arg) > H (His) Missense Variant
CACNA1S transcript variant X1 XM_005245478.3:c.1583G>T R [CGC] > L [CTC] Coding Sequence Variant
voltage-dependent L-type calcium channel subunit alpha-1S isoform X1 XP_005245535.1:p.Arg528Leu R (Arg) > L (Leu) Missense Variant
CACNA1S transcript variant X1 XM_005245478.3:c.1583G>A R [CGC] > H [CAC] Coding Sequence Variant
voltage-dependent L-type calcium channel subunit alpha-1S isoform X1 XP_005245535.1:p.Arg528His R (Arg) > H (His) Missense 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: A (allele ID: 447399 )
ClinVar Accession Disease Names Clinical Significance
RCV000549801.1 Hypokalemic periodic paralysis 1,Malignant hyperthermia susceptibility type 5 Uncertain-Significance
Allele: T (allele ID: 32664 )
ClinVar Accession Disease Names Clinical Significance
RCV000019192.27 Hypokalemic periodic paralysis 1 Pathogenic
RCV000414449.2 not provided Pathogenic
RCV000627794.2 Hypokalemic periodic paralysis 1,Malignant hyperthermia susceptibility type 5 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251124 C=0.99999 A=0.00001
gnomAD - Exomes European Sub 135098 C=0.99998 A=0.00002
gnomAD - Exomes Asian Sub 49006 C=1.0000 A=0.0000
gnomAD - Exomes American Sub 34580 C=1.0000 A=0.0000
gnomAD - Exomes African Sub 16248 C=1.0000 A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10068 C=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6124 C=1.000 A=0.000
TopMed Global Study-wide 125568 C=0.99996 T=0.00001, A=0.00003
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 C= A T Note
GRCh38.p12 chr 1 NC_000001.11:g.20...

NC_000001.11:g.201077915=

NC_000001.11:g.20...

NC_000001.11:g.201077915C>A

NC_000001.11:g.20...

NC_000001.11:g.201077915C>T

GRCh37.p13 chr 1 NC_000001.10:g.20...

NC_000001.10:g.201047043=

NC_000001.10:g.20...

NC_000001.10:g.201047043C>A

NC_000001.10:g.20...

NC_000001.10:g.201047043C>T

CACNA1S RefSeqGene NG_009816.2:g.39652= NG_009816.2:g.396...

NG_009816.2:g.39652G>T

NG_009816.2:g.396...

NG_009816.2:g.39652G>A

CACNA1S RefSeqGene NG_009816.1:g.39652= NG_009816.1:g.396...

NG_009816.1:g.39652G>T

NG_009816.1:g.396...

NG_009816.1:g.39652G>A

CACNA1S transcript NM_000069.3:c.1583= NM_000069.3:c.158...

NM_000069.3:c.1583G>T

NM_000069.3:c.158...

NM_000069.3:c.1583G>A

CACNA1S transcript NM_000069.2:c.1583= NM_000069.2:c.158...

NM_000069.2:c.1583G>T

NM_000069.2:c.158...

NM_000069.2:c.1583G>A

CACNA1S transcript variant X1 XM_005245478.3:c....

XM_005245478.3:c.1583=

XM_005245478.3:c....

XM_005245478.3:c.1583G>T

XM_005245478.3:c....

XM_005245478.3:c.1583G>A

CACNA1S transcript variant X1 XM_005245478.1:c....

XM_005245478.1:c.1583=

XM_005245478.1:c....

XM_005245478.1:c.1583G>T

XM_005245478.1:c....

XM_005245478.1:c.1583G>A

voltage-dependent L-type calcium channel subunit alpha-1S NP_000060.2:p.Arg...

NP_000060.2:p.Arg528=

NP_000060.2:p.Arg...

NP_000060.2:p.Arg528Leu

NP_000060.2:p.Arg...

NP_000060.2:p.Arg528His

voltage-dependent L-type calcium channel subunit alpha-1S isoform X1 XP_005245535.1:p....

XP_005245535.1:p.Arg528=

XP_005245535.1:p....

XP_005245535.1:p.Arg528Leu

XP_005245535.1:p....

XP_005245535.1:p.Arg528His

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#.

7 SubSNP, 2 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENEREVIEWS ss179362448 Nov 18, 2009 (131)
2 OMIM-CURATED-RECORDS ss275514022 Nov 22, 2010 (133)
3 HUMAN_LONGEVITY ss2169209912 Dec 20, 2016 (150)
4 GNOMAD ss2732169445 Nov 08, 2017 (151)
5 TOPMED ss3100588997 Nov 08, 2017 (151)
6 TOPMED ss3100588998 Nov 08, 2017 (151)
7 ILLUMINA ss3725094599 Jul 12, 2019 (153)
8 gnomAD - Exomes NC_000001.10 - 201047043 Jul 12, 2019 (153)
9 TopMed NC_000001.11 - 201077915 Oct 11, 2018 (152)
10 ClinVar RCV000019192.27 Oct 11, 2018 (152)
11 ClinVar RCV000414449.2 Jul 12, 2019 (153)
12 ClinVar RCV000549801.1 Oct 11, 2018 (152)
13 ClinVar RCV000627794.2 Jul 12, 2019 (153)
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
1202117, ss2732169445 NC_000001.10:201047042:C:A NC_000001.11:201077914:C:A (self)
RCV000549801.1, 27259713, ss2169209912, ss3100588997 NC_000001.11:201077914:C:A NC_000001.11:201077914:C:A (self)
RCV000019192.27, RCV000414449.2, RCV000627794.2, 27259713, ss179362448, ss275514022, ss3100588998, ss3725094599 NC_000001.11:201077914:C:T NC_000001.11:201077914:C:T (self)
Help

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

6 citations for rs80338777
PMID Title Author Year Journal
7847370 Hypokalemic periodic paralysis and the dihydropyridine receptor (CACNL1A3): genotype/phenotype correlations for two predominant mutations and evidence for the absence of a founder effect in 16 caucasian families. Elbaz A et al. 1995 American journal of human genetics
7897626 Mutation in DHP receptor alpha 1 subunit (CACLN1A3) gene in a Dutch family with hypokalaemic periodic paralysis. Boerman RH et al. 1995 Journal of medical genetics
7987325 A calcium channel mutation causing hypokalemic periodic paralysis. Jurkat-Rott K et al. 1994 Human molecular genetics
10074484 Impairment of skeletal muscle adenosine triphosphate-sensitive K+ channels in patients with hypokalemic periodic paralysis. Tricarico D et al. 1999 The Journal of clinical investigation
11353725 Hypokalaemic periodic paralysis type 2 caused by mutations at codon 672 in the muscle sodium channel gene SCN4A. Sternberg D et al. 2001 Brain
20301512 Hypokalemic Periodic Paralysis Weber F et al. 1993 GeneReviews®

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.post288+114f6e8