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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.

rs760238687

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:93922610 (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
A=0.000068 (18/264690, TOPMED)
A=0.000028 (7/251374, GnomAD_exome)
A=0.000043 (6/140136, GnomAD) (+ 3 more)
A=0.000033 (4/121302, ExAC)
A=0.00003 (2/78702, PAGE_STUDY)
A=0.00000 (0/14710, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PDP1 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14710 G=1.00000 A=0.00000
European Sub 9768 G=1.0000 A=0.0000
African Sub 3332 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 3218 G=1.0000 A=0.0000
Asian Sub 146 G=1.000 A=0.000
East Asian Sub 120 G=1.000 A=0.000
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 604 G=1.000 A=0.000


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
TopMed Global Study-wide 264690 G=0.999932 A=0.000068
gnomAD - Exomes Global Study-wide 251374 G=0.999972 A=0.000028
gnomAD - Exomes European Sub 135312 G=0.999970 A=0.000030
gnomAD - Exomes Asian Sub 49008 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34584 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16252 G=0.99982 A=0.00018
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6140 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140136 G=0.999957 A=0.000043
gnomAD - Genomes European Sub 75916 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 41984 G=0.99986 A=0.00014
gnomAD - Genomes American Sub 13628 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
ExAC Global Study-wide 121302 G=0.999967 A=0.000033
ExAC Europe Sub 73294 G=0.99999 A=0.00001
ExAC Asian Sub 25152 G=1.00000 A=0.00000
ExAC American Sub 11560 G=1.00000 A=0.00000
ExAC African Sub 10390 G=0.99971 A=0.00029
ExAC Other Sub 906 G=1.000 A=0.000
The PAGE Study Global Study-wide 78702 G=0.99997 A=0.00003
The PAGE Study AfricanAmerican Sub 32516 G=0.99997 A=0.00003
The PAGE Study Mexican Sub 10810 G=0.99991 A=0.00009
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 14710 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9768 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 3332 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 604 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
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 8 NC_000008.11:g.93922610G>A
GRCh37.p13 chr 8 NC_000008.10:g.94934838G>A
PDP1 RefSeqGene NG_012233.1:g.10677G>A
Gene: PDP1, pyruvate dehydrogenase phosphatase catalytic subunit 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PDP1 transcript variant 5 NM_018444.4:c.551G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 3 NP_060914.2:p.Arg184Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant 3 NM_001161780.2:c.626G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 2 NP_001155252.1:p.Arg209Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant 4 NM_001161781.2:c.551G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 3 NP_001155253.1:p.Arg184Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant 2 NM_001161779.2:c.626G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 2 NP_001155251.1:p.Arg209Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant X1 XM_017013588.2:c.713G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X1 XP_016869077.1:p.Arg238Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant X2 XM_047421904.1:c.605G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X2 XP_047277860.1:p.Arg202Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant X3 XM_047421905.1:c.605G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X2 XP_047277861.1:p.Arg202Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant X4 XM_047421906.1:c.551G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277862.1:p.Arg184Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant X5 XM_047421907.1:c.551G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277863.1:p.Arg184Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant X6 XM_047421908.1:c.551G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277864.1:p.Arg184Gln R (Arg) > Q (Gln) Missense Variant
PDP1 transcript variant X7 XM_047421909.1:c.551G>A R [CGG] > Q [CAG] Coding Sequence Variant
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277865.1:p.Arg184Gln R (Arg) > Q (Gln) 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.

Not Reported in ClinVar
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 8 NC_000008.11:g.93922610= NC_000008.11:g.93922610G>A
GRCh37.p13 chr 8 NC_000008.10:g.94934838= NC_000008.10:g.94934838G>A
PDP1 RefSeqGene NG_012233.1:g.10677= NG_012233.1:g.10677G>A
PDP1 transcript variant 5 NM_018444.4:c.551= NM_018444.4:c.551G>A
PDP1 transcript variant 5 NM_018444.3:c.551= NM_018444.3:c.551G>A
PDP1 transcript variant 2 NM_001161779.2:c.626= NM_001161779.2:c.626G>A
PDP1 transcript variant 2 NM_001161779.1:c.626= NM_001161779.1:c.626G>A
PDP1 transcript variant 4 NM_001161781.2:c.551= NM_001161781.2:c.551G>A
PDP1 transcript variant 4 NM_001161781.1:c.551= NM_001161781.1:c.551G>A
PDP1 transcript variant 3 NM_001161780.2:c.626= NM_001161780.2:c.626G>A
PDP1 transcript variant 3 NM_001161780.1:c.626= NM_001161780.1:c.626G>A
PDP1 transcript variant X1 XM_017013588.2:c.713= XM_017013588.2:c.713G>A
PDP1 transcript variant X1 XM_017013588.1:c.713= XM_017013588.1:c.713G>A
PDP1 transcript variant X7 XM_047421909.1:c.551= XM_047421909.1:c.551G>A
PDP1 transcript variant X5 XM_047421907.1:c.551= XM_047421907.1:c.551G>A
PDP1 transcript variant X4 XM_047421906.1:c.551= XM_047421906.1:c.551G>A
PDP1 transcript variant X6 XM_047421908.1:c.551= XM_047421908.1:c.551G>A
PDP1 transcript variant X3 XM_047421905.1:c.605= XM_047421905.1:c.605G>A
PDP1 transcript variant X2 XM_047421904.1:c.605= XM_047421904.1:c.605G>A
PDP1 transcript variant 1 NM_001161778.1:c.728= NM_001161778.1:c.728G>A
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 3 NP_060914.2:p.Arg184= NP_060914.2:p.Arg184Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 2 NP_001155251.1:p.Arg209= NP_001155251.1:p.Arg209Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 3 NP_001155253.1:p.Arg184= NP_001155253.1:p.Arg184Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 2 NP_001155252.1:p.Arg209= NP_001155252.1:p.Arg209Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X1 XP_016869077.1:p.Arg238= XP_016869077.1:p.Arg238Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277865.1:p.Arg184= XP_047277865.1:p.Arg184Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277863.1:p.Arg184= XP_047277863.1:p.Arg184Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277862.1:p.Arg184= XP_047277862.1:p.Arg184Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3 XP_047277864.1:p.Arg184= XP_047277864.1:p.Arg184Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X2 XP_047277861.1:p.Arg202= XP_047277861.1:p.Arg202Gln
pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X2 XP_047277860.1:p.Arg202= XP_047277860.1:p.Arg202Gln
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#.

9 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1689253625 Apr 01, 2015 (144)
2 ILLUMINA ss1959127544 Feb 12, 2016 (147)
3 GNOMAD ss2737248647 Nov 08, 2017 (151)
4 ILLUMINA ss3022864481 Nov 08, 2017 (151)
5 ILLUMINA ss3653409539 Oct 12, 2018 (152)
6 ILLUMINA ss3726554930 Jul 13, 2019 (153)
7 PAGE_CC ss3771455854 Jul 13, 2019 (153)
8 GNOMAD ss4189400615 Apr 26, 2021 (155)
9 TOPMED ss4796166546 Apr 26, 2021 (155)
10 ExAC NC_000008.10 - 94934838 Oct 12, 2018 (152)
11 gnomAD - Genomes NC_000008.11 - 93922610 Apr 26, 2021 (155)
12 gnomAD - Exomes NC_000008.10 - 94934838 Jul 13, 2019 (153)
13 The PAGE Study NC_000008.11 - 93922610 Jul 13, 2019 (153)
14 TopMed NC_000008.11 - 93922610 Apr 26, 2021 (155)
15 ALFA NC_000008.11 - 93922610 Apr 26, 2021 (155)
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
9358940, 6421258, ss1689253625, ss1959127544, ss2737248647, ss3022864481, ss3653409539 NC_000008.10:94934837:G:A NC_000008.11:93922609:G:A (self)
304403281, 677323, 633544106, 7945964180, ss3726554930, ss3771455854, ss4189400615, ss4796166546 NC_000008.11:93922609:G:A NC_000008.11:93922609: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.

No publications for rs760238687

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