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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.

rs199476097

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr16:2090468 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
PKD1 : Stop Gained
MIR1225 : 2KB Upstream Variant
LOC105371049 : 2KB Upstream Variant
Publications
1 citation
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 16 NC_000016.10:g.2090468A>T
GRCh37.p13 chr 16 NC_000016.9:g.2140469A>T
PKD1 RefSeqGene NG_008617.1:g.52753T>A
TSC2 RefSeqGene (LRG_487) NG_005895.1:g.46163A>T
Gene: PKD1, polycystin 1, transient receptor potential channel interacting (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PKD1 transcript variant 1 NM_001009944.2:c.12261T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform 1 precursor NP_001009944.2:p.Cys408...

NP_001009944.2:p.Cys4087Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant 2 NM_000296.3:c.12258T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform 2 precursor NP_000287.3:p.Cys4086Ter C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X3 XM_011522529.2:c.12312T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X3 XP_011520831.1:p.Cys410...

XP_011520831.1:p.Cys4104Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X7 XM_011522537.2:c.9339T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X7 XP_011520839.1:p.Cys311...

XP_011520839.1:p.Cys3113Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X8 XM_005255370.3:c.9216T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X8 XP_005255427.1:p.Cys307...

XP_005255427.1:p.Cys3072Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X1 XM_024450298.1:c.12381T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X1 XP_024306066.1:p.Cys412...

XP_024306066.1:p.Cys4127Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X2 XM_011522528.3:c.12315T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X2 XP_011520830.1:p.Cys410...

XP_011520830.1:p.Cys4105Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X4 XM_024450299.1:c.12309T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X4 XP_024306067.1:p.Cys410...

XP_024306067.1:p.Cys4103Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X5 XM_024450300.1:c.12171T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X5 XP_024306068.1:p.Cys405...

XP_024306068.1:p.Cys4057Ter

C (Cys) > * (Ter) Stop Gained
PKD1 transcript variant X6 XM_024450301.1:c.10257T>A C [TGT] > * [TGA] Coding Sequence Variant
polycystin-1 isoform X6 XP_024306069.1:p.Cys341...

XP_024306069.1:p.Cys3419Ter

C (Cys) > * (Ter) Stop Gained
Gene: MIR1225, microRNA 1225 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR1225 transcript NR_030646.1:n. N/A Upstream Transcript Variant
Gene: LOC105371049, uncharacterized LOC105371049 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105371049 transcript NR_135175.1:n. N/A Upstream 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: T (allele ID: 23239 )
ClinVar Accession Disease Names Clinical Significance
RCV000008683.3 Polycystic kidney disease, adult type 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= T Note
GRCh38.p12 chr 16 NC_000016.10:g.2090468A= NC_000016.10:g.2090468A>T
GRCh37.p13 chr 16 NC_000016.9:g.2140469A= NC_000016.9:g.2140469A>T
PKD1 RefSeqGene NG_008617.1:g.52753T= NG_008617.1:g.52753T>A
PKD1 transcript variant 2 NM_000296.3:c.12258T= NM_000296.3:c.12258T>A
PKD1 transcript variant 1 NM_001009944.2:c.12261T= NM_001009944.2:c.12261T>A
TSC2 RefSeqGene (LRG_487) NG_005895.1:g.46163A= NG_005895.1:g.46163A>T
PKD1 transcript variant X2 XM_011522528.3:c.12315T= XM_011522528.3:c.12315T>A
PKD1 transcript variant X8 XM_005255370.3:c.9216T= XM_005255370.3:c.9216T>A
PKD1 transcript variant X5 XM_005255370.1:c.9216T= XM_005255370.1:c.9216T>A
PKD1 transcript variant X3 XM_011522529.2:c.12312T= XM_011522529.2:c.12312T>A
PKD1 transcript variant X7 XM_011522537.2:c.9339T= XM_011522537.2:c.9339T>A
PKD1 transcript variant X1 XM_024450298.1:c.12381T= XM_024450298.1:c.12381T>A
PKD1 transcript variant X5 XM_024450300.1:c.12171T= XM_024450300.1:c.12171T>A
PKD1 transcript variant X4 XM_024450299.1:c.12309T= XM_024450299.1:c.12309T>A
PKD1 transcript variant X6 XM_024450301.1:c.10257T= XM_024450301.1:c.10257T>A
polycystin-1 isoform 2 precursor NP_000287.3:p.Cys4086= NP_000287.3:p.Cys4086Ter
polycystin-1 isoform 1 precursor NP_001009944.2:p.Cys4087= NP_001009944.2:p.Cys408...

NP_001009944.2:p.Cys4087Ter

polycystin-1 isoform X2 XP_011520830.1:p.Cys4105= XP_011520830.1:p.Cys410...

XP_011520830.1:p.Cys4105Ter

polycystin-1 isoform X8 XP_005255427.1:p.Cys3072= XP_005255427.1:p.Cys307...

XP_005255427.1:p.Cys3072Ter

polycystin-1 isoform X3 XP_011520831.1:p.Cys4104= XP_011520831.1:p.Cys410...

XP_011520831.1:p.Cys4104Ter

polycystin-1 isoform X7 XP_011520839.1:p.Cys3113= XP_011520839.1:p.Cys311...

XP_011520839.1:p.Cys3113Ter

polycystin-1 isoform X1 XP_024306066.1:p.Cys4127= XP_024306066.1:p.Cys412...

XP_024306066.1:p.Cys4127Ter

polycystin-1 isoform X5 XP_024306068.1:p.Cys4057= XP_024306068.1:p.Cys405...

XP_024306068.1:p.Cys4057Ter

polycystin-1 isoform X4 XP_024306067.1:p.Cys4103= XP_024306067.1:p.Cys410...

XP_024306067.1:p.Cys4103Ter

polycystin-1 isoform X6 XP_024306069.1:p.Cys3419= XP_024306069.1:p.Cys341...

XP_024306069.1:p.Cys3419Ter

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#.

5 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss506984414 Apr 04, 2012 (136)
2 NCBI-CURATED-RECORDS ss537713439 Jan 04, 2013 (137)
3 ILLUMINA ss1959650757 Feb 12, 2016 (147)
4 ILLUMINA ss3021675173 Nov 08, 2017 (151)
5 ILLUMINA ss3652079003 Oct 12, 2018 (152)
6 ClinVar RCV000008683.3 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
ss1959650757, ss3021675173, ss3652079003 NC_000016.9:2140468:A:T NC_000016.10:2090467:A:T (self)
RCV000008683.3, ss506984414, ss537713439 NC_000016.10:2090467:A:T NC_000016.10:2090467:A:T (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 rs199476097
PMID Title Author Year Journal
8792818 Detection of a novel nonsense mutation and an intragenic polymorphism in the PKD1 gene of a Cypriot family with autosomal dominant polycystic kidney disease. Neophytou P et al. 1996 Human 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: 2.0.1.post104+4a6ee9c