Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs148463199

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:3674681 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000033 (6/183465, GnomAD_exome)
A=0.00002 (2/87748, ExAC)
A=0.00000 (0/14050, ALFA) (+ 2 more)
T=0.00000 (0/14050, ALFA)
A=0.00019 (2/10563, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRKX : 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 14050 G=1.00000 A=0.00000, T=0.00000
European Sub 9690 G=1.0000 A=0.0000, T=0.0000
African Sub 2898 G=1.0000 A=0.0000, T=0.0000
African Others Sub 114 G=1.000 A=0.000, T=0.000
African American Sub 2784 G=1.0000 A=0.0000, T=0.0000
Asian Sub 112 G=1.000 A=0.000, T=0.000
East Asian Sub 86 G=1.00 A=0.00, T=0.00
Other Asian Sub 26 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 G=1.000 A=0.000, T=0.000
South Asian Sub 98 G=1.00 A=0.00, T=0.00
Other Sub 496 G=1.000 A=0.000, T=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
gnomAD - Exomes Global Study-wide 183465 G=0.999967 A=0.000033
gnomAD - Exomes European Sub 97926 G=0.99996 A=0.00004
gnomAD - Exomes Asian Sub 32941 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 27418 G=0.99996 A=0.00004
gnomAD - Exomes African Sub 13163 G=0.99992 A=0.00008
gnomAD - Exomes Ashkenazi Jewish Sub 7487 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4530 G=1.0000 A=0.0000
ExAC Global Study-wide 87748 G=0.99998 A=0.00002
ExAC Europe Sub 52515 G=1.00000 A=0.00000
ExAC Asian Sub 16761 G=1.00000 A=0.00000
ExAC American Sub 9321 G=0.9999 A=0.0001
ExAC African Sub 8518 G=0.9999 A=0.0001
ExAC Other Sub 633 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00, T=0.00
GO Exome Sequencing Project Global Study-wide 10563 G=0.99981 A=0.00019
GO Exome Sequencing Project European American Sub 6728 G=0.9997 A=0.0003
GO Exome Sequencing Project African American Sub 3835 G=1.0000 A=0.0000
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 X NC_000023.11:g.3674681G>A
GRCh38.p14 chr X NC_000023.11:g.3674681G>T
GRCh37.p13 chr X NC_000023.10:g.3592722G>A
GRCh37.p13 chr X NC_000023.10:g.3592722G>T
PRKX RefSeqGene NG_016716.1:g.43954C>T
PRKX RefSeqGene NG_016716.1:g.43954C>A
Gene: PRKX, protein kinase X-linked (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRKX transcript NM_005044.5:c.252C>T D [GAC] > D [GAT] Coding Sequence Variant
cAMP-dependent protein kinase catalytic subunit PRKX NP_005035.1:p.Asp84= D (Asp) > D (Asp) Synonymous Variant
PRKX transcript NM_005044.5:c.252C>A D [GAC] > E [GAA] Coding Sequence Variant
cAMP-dependent protein kinase catalytic subunit PRKX NP_005035.1:p.Asp84Glu D (Asp) > E (Glu) 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 T
GRCh38.p14 chr X NC_000023.11:g.3674681= NC_000023.11:g.3674681G>A NC_000023.11:g.3674681G>T
GRCh37.p13 chr X NC_000023.10:g.3592722= NC_000023.10:g.3592722G>A NC_000023.10:g.3592722G>T
PRKX RefSeqGene NG_016716.1:g.43954= NG_016716.1:g.43954C>T NG_016716.1:g.43954C>A
PRKX transcript NM_005044.5:c.252= NM_005044.5:c.252C>T NM_005044.5:c.252C>A
PRKX transcript NM_005044.4:c.252= NM_005044.4:c.252C>T NM_005044.4:c.252C>A
cAMP-dependent protein kinase catalytic subunit PRKX NP_005035.1:p.Asp84= NP_005035.1:p.Asp84= NP_005035.1:p.Asp84Glu
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#.

8 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342549075 May 09, 2011 (134)
2 EVA_EXAC ss1694450453 Apr 01, 2015 (144)
3 GNOMAD ss2745295876 Nov 08, 2017 (151)
4 EVA ss3825471034 Apr 27, 2020 (154)
5 GNOMAD ss4367401191 Apr 26, 2021 (155)
6 GNOMAD ss4367401192 Apr 26, 2021 (155)
7 TOPMED ss5114230847 Apr 26, 2021 (155)
8 TOPMED ss5114230848 Apr 26, 2021 (155)
9 ExAC NC_000023.10 - 3592722 Oct 12, 2018 (152)
10 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 574266185 (NC_000023.11:3674680:G:A 4/103730)
Row 574266186 (NC_000023.11:3674680:G:T 1/103730)

- Apr 26, 2021 (155)
11 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 574266185 (NC_000023.11:3674680:G:A 4/103730)
Row 574266186 (NC_000023.11:3674680:G:T 1/103730)

- Apr 26, 2021 (155)
12 gnomAD - Exomes NC_000023.10 - 3592722 Jul 13, 2019 (153)
13 GO Exome Sequencing Project NC_000023.10 - 3592722 Oct 12, 2018 (152)
14 TopMed

Submission ignored due to conflicting rows:
Row 677837204 (NC_000023.11:3674680:G:A 19/264690)
Row 677837205 (NC_000023.11:3674680:G:T 1/264690)

- Apr 26, 2021 (155)
15 TopMed

Submission ignored due to conflicting rows:
Row 677837204 (NC_000023.11:3674680:G:A 19/264690)
Row 677837205 (NC_000023.11:3674680:G:T 1/264690)

- Apr 26, 2021 (155)
16 ALFA NC_000023.11 - 3674681 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
9946940, 14632493, 1927839, ss342549075, ss1694450453, ss2745295876, ss3825471034 NC_000023.10:3592721:G:A NC_000023.11:3674680:G:A (self)
5783449878, ss4367401191, ss5114230847 NC_000023.11:3674680:G:A NC_000023.11:3674680:G:A (self)
5783449878, ss4367401192, ss5114230848 NC_000023.11:3674680:G:T NC_000023.11:3674680:G:T (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 rs148463199

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