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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.

rs199472804

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr11:2776997 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
KCNQ1 : Missense Variant
Publications
8 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 11 NC_000011.10:g.2776997C>A
GRCh38.p7 chr 11 NC_000011.10:g.2776997C>T
GRCh37.p13 chr 11 NC_000011.9:g.2798227C>A
GRCh37.p13 chr 11 NC_000011.9:g.2798227C>T
KCNQ1 RefSeqGene (LRG_287) NG_008935.1:g.337007C>A
KCNQ1 RefSeqGene (LRG_287) NG_008935.1:g.337007C>T
GRCh38.p7 chr 11 alt locus HSCHR11_1_CTG7 NT_187585.1:g.9184C>A
GRCh38.p7 chr 11 alt locus HSCHR11_1_CTG7 NT_187585.1:g.9184C>T
Gene: KCNQ1, potassium voltage-gated channel subfamily Q member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
KCNQ1 transcript variant 2 NM_181798.1:c.131...

NM_181798.1:c.1316C>A

S [TCC] > Y [TAC] Coding Sequence Variant
potassium voltage-gated channel subfamily KQT member 1 isoform 2 precursor NP_861463.1:p.Ser...

NP_861463.1:p.Ser439Tyr

S (Ser) > Y (Tyr) Missense Variant
KCNQ1 transcript variant 2 NM_181798.1:c.131...

NM_181798.1:c.1316C>T

S [TCC] > F [TTC] Coding Sequence Variant
potassium voltage-gated channel subfamily KQT member 1 isoform 2 precursor NP_861463.1:p.Ser...

NP_861463.1:p.Ser439Phe

S (Ser) > F (Phe) Missense Variant
KCNQ1 transcript variant 1 NM_000218.2:c.169...

NM_000218.2:c.1697C>A

S [TCC] > Y [TAC] Coding Sequence Variant
potassium voltage-gated channel subfamily KQT member 1 isoform 1 NP_000209.2:p.Ser...

NP_000209.2:p.Ser566Tyr

S (Ser) > Y (Tyr) Missense Variant
KCNQ1 transcript variant 1 NM_000218.2:c.169...

NM_000218.2:c.1697C>T

S [TCC] > F [TTC] Coding Sequence Variant
potassium voltage-gated channel subfamily KQT member 1 isoform 1 NP_000209.2:p.Ser...

NP_000209.2:p.Ser566Phe

S (Ser) > F (Phe) 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: 67673 )
ClinVar Accession Disease Names Clinical Significance
RCV000046014.3 Long QT syndrome Uncertain-Significance
RCV000057618.3 Congenital long QT syndrome Not-Provided
RCV000505737.2 not provided Likely-Pathogenic
Allele: T (allele ID: 67674 )
ClinVar Accession Disease Names Clinical Significance
RCV000046015.5 Long QT syndrome Likely-Pathogenic
RCV000057619.3 Congenital long QT syndrome Not-Provided
RCV000223686.2 not provided Likely-Pathogenic
RCV000477954.1 Long QT syndrome 1 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 C= A T Note
GRCh38.p7 chr 11 NC_000011.10:g.27...

NC_000011.10:g.2776997C=

NC_000011.10:g.27...

NC_000011.10:g.2776997C>A

NC_000011.10:g.27...

NC_000011.10:g.2776997C>T

GRCh37.p13 chr 11 NC_000011.9:g.279...

NC_000011.9:g.2798227C=

NC_000011.9:g.279...

NC_000011.9:g.2798227C>A

NC_000011.9:g.279...

NC_000011.9:g.2798227C>T

KCNQ1 RefSeqGene (LRG_287) NG_008935.1:g.337...

NG_008935.1:g.337007C=

NG_008935.1:g.337...

NG_008935.1:g.337007C>A

NG_008935.1:g.337...

NG_008935.1:g.337007C>T

KCNQ1 transcript variant 1 NM_000218.2:c.1697C= NM_000218.2:c.169...

NM_000218.2:c.1697C>A

NM_000218.2:c.169...

NM_000218.2:c.1697C>T

KCNQ1 transcript variant 2 NM_181798.1:c.1316C= NM_181798.1:c.131...

NM_181798.1:c.1316C>A

NM_181798.1:c.131...

NM_181798.1:c.1316C>T

GRCh38.p7 chr 11 alt locus HSCHR11_1_CTG7 NT_187585.1:g.9184C= NT_187585.1:g.918...

NT_187585.1:g.9184C>A

NT_187585.1:g.918...

NT_187585.1:g.9184C>T

potassium voltage-gated channel subfamily KQT member 1 isoform 1 NP_000209.2:p.Ser...

NP_000209.2:p.Ser566=

NP_000209.2:p.Ser...

NP_000209.2:p.Ser566Tyr

NP_000209.2:p.Ser...

NP_000209.2:p.Ser566Phe

potassium voltage-gated channel subfamily KQT member 1 isoform 2 precursor NP_861463.1:p.Ser...

NP_861463.1:p.Ser439=

NP_861463.1:p.Ser...

NP_861463.1:p.Ser439Tyr

NP_861463.1:p.Ser...

NP_861463.1:p.Ser439Phe

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#.

2 SubSNP, 7 ClinVar submissions
No Submitter Submission ID Date (Build)
1 RBH_CV_BRU ss487103643 Mar 09, 2012 (136)
2 RBH_CV_BRU ss487104345 Mar 09, 2012 (136)
3 ClinVar RCV000046014.3 Jul 20, 2018 (151)
4 ClinVar RCV000046015.5 Jul 20, 2018 (151)
5 ClinVar RCV000057618.3 Jul 20, 2018 (151)
6 ClinVar RCV000057619.3 Jul 20, 2018 (151)
7 ClinVar RCV000223686.2 Jul 20, 2018 (151)
8 ClinVar RCV000477954.1 Jul 20, 2018 (151)
9 ClinVar RCV000505737.2 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
ss487103643, ss487104345 NC_000011.10:2776996:C= NC_000011.10:2776996:C= (self)
RCV000046014.3, RCV000057618.3, RCV000505737.2, ss487104345 NC_000011.10:2776996:C>A NC_000011.10:2776996:C>A (self)
RCV000046015.5, RCV000057619.3, RCV000223686.2, RCV000477954.1, ss487103643 NC_000011.10:2776996:C>T NC_000011.10:2776996: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.

8 citations for rs199472804
PMID Title Author Year Journal
10973849 Spectrum of mutations in long-QT syndrome genes. KVLQT1, HERG, SCN5A, KCNE1, and KCNE2. Splawski I et al. 2000 Circulation
14678125 Location of mutation in the KCNQ1 and phenotypic presentation of long QT syndrome. Zareba W et al. 2003 Journal of cardiovascular electrophysiology
15840476 Compendium of cardiac channel mutations in 541 consecutive unrelated patients referred for long QT syndrome genetic testing. Tester DJ et al. 2005 Heart rhythm
17470695 Clinical aspects of type-1 long-QT syndrome by location, coding type, and biophysical function of mutations involving the KCNQ1 gene. Moss AJ et al. 2007 Circulation
19716085 Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Kapplinger JD et al. 2009 Heart rhythm
19841300 Genetic testing for long-QT syndrome: distinguishing pathogenic mutations from benign variants. Kapa S et al. 2009 Circulation
22581653 Paralogous annotation of disease-causing variants in long QT syndrome genes. Ware JS et al. 2012 Human mutation
22949429 Phylogenetic and physicochemical analyses enhance the classification of rare nonsynonymous single nucleotide variants in type 1 and 2 long-QT syndrome. Giudicessi JR et al. 2012 Circulation. Cardiovascular genetics

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.post833+d3ba21e