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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.

rs1959440

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr14:29739424 (GRCh38.p13) 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
T=0.495976 (131280/264690, TOPMED)
T=0.41700 (38716/92844, ALFA)
T=0.37578 (6298/16760, 8.3KJPN) (+ 13 more)
G=0.4940 (2474/5008, 1000G)
T=0.4638 (2078/4480, Estonian)
T=0.4323 (1666/3854, ALSPAC)
T=0.4439 (1646/3708, TWINSUK)
T=0.2884 (845/2930, KOREAN)
T=0.2942 (539/1832, Korea1K)
T=0.414 (413/998, GoNL)
T=0.377 (226/600, NorthernSweden)
G=0.286 (114/398, SGDP_PRJ)
T=0.475 (150/316, HapMap)
G=0.454 (98/216, Qatari)
G=0.39 (17/44, Siberian)
T=0.35 (14/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRKD1 : Intron Variant
Publications
0 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.p13 chr 14 NC_000014.9:g.29739424G>A
GRCh38.p13 chr 14 NC_000014.9:g.29739424G>T
GRCh37.p13 chr 14 NC_000014.8:g.30208630G>A
GRCh37.p13 chr 14 NC_000014.8:g.30208630G>T
PRKD1 RefSeqGene NG_052879.1:g.193270C>T
PRKD1 RefSeqGene NG_052879.1:g.193270C>A
Gene: PRKD1, protein kinase D1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRKD1 transcript variant 1 NM_001330069.2:c.265-1375…

NM_001330069.2:c.265-13750C>T

N/A Intron Variant
PRKD1 transcript variant 3 NM_001348390.1:c.-24-1375…

NM_001348390.1:c.-24-13750C>T

N/A Intron Variant
PRKD1 transcript variant 2 NM_002742.3:c.265-13750C>T N/A Intron Variant
PRKD1 transcript variant X1 XM_011536965.2:c.-24-1375…

XM_011536965.2:c.-24-13750C>T

N/A Intron Variant
PRKD1 transcript variant X3 XM_017021462.1:c.-307-137…

XM_017021462.1:c.-307-13750C>T

N/A Intron Variant
PRKD1 transcript variant X2 XR_943493.2:n. N/A Intron 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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 92844 G=0.58300 A=0.00000, T=0.41700
European Sub 82038 G=0.58842 A=0.00000, T=0.41158
African Sub 2682 G=0.4224 A=0.0000, T=0.5776
African Others Sub 102 G=0.314 A=0.000, T=0.686
African American Sub 2580 G=0.4267 A=0.0000, T=0.5733
Asian Sub 282 G=0.812 A=0.000, T=0.188
East Asian Sub 198 G=0.828 A=0.000, T=0.172
Other Asian Sub 84 G=0.77 A=0.00, T=0.23
Latin American 1 Sub 528 G=0.566 A=0.000, T=0.434
Latin American 2 Sub 1622 G=0.5691 A=0.0000, T=0.4309
South Asian Sub 90 G=0.54 A=0.00, T=0.46
Other Sub 5602 G=0.5752 A=0.0000, T=0.4248


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=0.504024 T=0.495976
8.3KJPN JAPANESE Study-wide 16760 G=0.62422 T=0.37578
1000Genomes Global Study-wide 5008 G=0.4940 T=0.5060
1000Genomes African Sub 1322 G=0.2882 T=0.7118
1000Genomes East Asian Sub 1008 G=0.7589 T=0.2411
1000Genomes Europe Sub 1006 G=0.5616 T=0.4384
1000Genomes South Asian Sub 978 G=0.399 T=0.601
1000Genomes American Sub 694 G=0.537 T=0.463
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5362 T=0.4638
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5677 T=0.4323
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5561 T=0.4439
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7116 A=0.0000, T=0.2884
Korean Genome Project KOREAN Study-wide 1832 G=0.7058 T=0.2942
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.586 T=0.414
Northern Sweden ACPOP Study-wide 600 G=0.623 T=0.377
SGDP_PRJ Global Study-wide 398 G=0.286 T=0.714
HapMap Global Study-wide 316 G=0.525 T=0.475
HapMap African Sub 116 G=0.379 T=0.621
HapMap American Sub 112 G=0.571 T=0.429
HapMap Asian Sub 88 G=0.66 T=0.34
Qatari Global Study-wide 216 G=0.454 T=0.546
Siberian Global Study-wide 44 G=0.39 T=0.61
The Danish reference pan genome Danish Study-wide 40 G=0.65 T=0.35
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.p13 chr 14 NC_000014.9:g.29739424= NC_000014.9:g.29739424G>A NC_000014.9:g.29739424G>T
GRCh37.p13 chr 14 NC_000014.8:g.30208630= NC_000014.8:g.30208630G>A NC_000014.8:g.30208630G>T
PRKD1 RefSeqGene NG_052879.1:g.193270= NG_052879.1:g.193270C>T NG_052879.1:g.193270C>A
PRKD1 transcript variant 1 NM_001330069.2:c.265-13750= NM_001330069.2:c.265-13750C>T NM_001330069.2:c.265-13750C>A
PRKD1 transcript variant 3 NM_001348390.1:c.-24-13750= NM_001348390.1:c.-24-13750C>T NM_001348390.1:c.-24-13750C>A
PRKD1 transcript variant 2 NM_002742.2:c.265-13750= NM_002742.2:c.265-13750C>T NM_002742.2:c.265-13750C>A
PRKD1 transcript variant 2 NM_002742.3:c.265-13750= NM_002742.3:c.265-13750C>T NM_002742.3:c.265-13750C>A
PRKD1 transcript variant X1 XM_005267859.1:c.265-13750= XM_005267859.1:c.265-13750C>T XM_005267859.1:c.265-13750C>A
PRKD1 transcript variant X1 XM_011536965.2:c.-24-13750= XM_011536965.2:c.-24-13750C>T XM_011536965.2:c.-24-13750C>A
PRKD1 transcript variant X3 XM_017021462.1:c.-307-13750= XM_017021462.1:c.-307-13750C>T XM_017021462.1:c.-307-13750C>A
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#.

93 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2854951 Jan 12, 2001 (92)
2 SC_JCM ss6160335 Feb 20, 2003 (111)
3 WI_SSAHASNP ss6896430 Feb 20, 2003 (111)
4 WI_SSAHASNP ss12297820 Jul 11, 2003 (116)
5 SSAHASNP ss21207949 Apr 05, 2004 (121)
6 PERLEGEN ss23577880 Sep 20, 2004 (123)
7 ABI ss43598593 Mar 13, 2006 (126)
8 EGP_SNPS ss70452589 May 18, 2007 (127)
9 HGSV ss81645587 Dec 16, 2007 (130)
10 BCMHGSC_JDW ss89894141 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss96903707 Feb 06, 2009 (130)
12 BGI ss103173036 Dec 01, 2009 (131)
13 1000GENOMES ss108211862 Jan 23, 2009 (130)
14 1000GENOMES ss113091531 Jan 25, 2009 (130)
15 ILLUMINA-UK ss118395325 Feb 14, 2009 (130)
16 ENSEMBL ss133894617 Dec 01, 2009 (131)
17 ENSEMBL ss143683281 Dec 01, 2009 (131)
18 ILLUMINA ss160481886 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167757627 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss169036586 Jul 04, 2010 (132)
21 BUSHMAN ss199876459 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss206957488 Jul 04, 2010 (132)
23 1000GENOMES ss226485672 Jul 14, 2010 (132)
24 1000GENOMES ss236479296 Jul 15, 2010 (132)
25 1000GENOMES ss242926176 Jul 15, 2010 (132)
26 GMI ss281940331 May 04, 2012 (137)
27 GMI ss286812552 Apr 25, 2013 (138)
28 PJP ss291692395 May 09, 2011 (134)
29 ILLUMINA ss480360765 May 04, 2012 (137)
30 ILLUMINA ss480372855 May 04, 2012 (137)
31 ILLUMINA ss481142942 Sep 08, 2015 (146)
32 ILLUMINA ss484977956 May 04, 2012 (137)
33 ILLUMINA ss537015186 Sep 08, 2015 (146)
34 TISHKOFF ss563997118 Apr 25, 2013 (138)
35 SSMP ss659660170 Apr 25, 2013 (138)
36 ILLUMINA ss778474321 Aug 21, 2014 (142)
37 ILLUMINA ss782935286 Aug 21, 2014 (142)
38 ILLUMINA ss783898019 Aug 21, 2014 (142)
39 ILLUMINA ss832190795 Apr 01, 2015 (144)
40 ILLUMINA ss833930130 Aug 21, 2014 (142)
41 EVA-GONL ss990976481 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1079525627 Aug 21, 2014 (142)
43 1000GENOMES ss1350369561 Aug 21, 2014 (142)
44 DDI ss1427372205 Apr 01, 2015 (144)
45 EVA_GENOME_DK ss1577146347 Apr 01, 2015 (144)
46 EVA_UK10K_ALSPAC ss1631401128 Apr 01, 2015 (144)
47 EVA_UK10K_TWINSUK ss1674395161 Apr 01, 2015 (144)
48 EVA_DECODE ss1694967928 Apr 01, 2015 (144)
49 ILLUMINA ss1752127816 Sep 08, 2015 (146)
50 HAMMER_LAB ss1807850641 Sep 08, 2015 (146)
51 WEILL_CORNELL_DGM ss1934352593 Feb 12, 2016 (147)
52 GENOMED ss1967924940 Jul 19, 2016 (147)
53 JJLAB ss2027950685 Sep 14, 2016 (149)
54 USC_VALOUEV ss2156322450 Dec 20, 2016 (150)
55 HUMAN_LONGEVITY ss2200668609 Dec 20, 2016 (150)
56 TOPMED ss2364969768 Dec 20, 2016 (150)
57 SYSTEMSBIOZJU ss2628464175 Nov 08, 2017 (151)
58 ILLUMINA ss2633131257 Nov 08, 2017 (151)
59 GRF ss2700738515 Nov 08, 2017 (151)
60 GNOMAD ss2925884741 Nov 08, 2017 (151)
61 SWEGEN ss3011941433 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3027798237 Nov 08, 2017 (151)
63 TOPMED ss3207027426 Nov 08, 2017 (151)
64 TOPMED ss3207027427 Nov 08, 2017 (151)
65 CSHL ss3350730797 Nov 08, 2017 (151)
66 ILLUMINA ss3627184850 Oct 12, 2018 (152)
67 ILLUMINA ss3631130518 Oct 12, 2018 (152)
68 ILLUMINA ss3633070942 Oct 12, 2018 (152)
69 ILLUMINA ss3633774141 Oct 12, 2018 (152)
70 ILLUMINA ss3634570180 Oct 12, 2018 (152)
71 ILLUMINA ss3635463742 Oct 12, 2018 (152)
72 ILLUMINA ss3636259165 Oct 12, 2018 (152)
73 ILLUMINA ss3637214892 Oct 12, 2018 (152)
74 ILLUMINA ss3640277508 Oct 12, 2018 (152)
75 URBANLAB ss3650171066 Oct 12, 2018 (152)
76 EGCUT_WGS ss3679182945 Jul 13, 2019 (153)
77 EVA_DECODE ss3696364925 Jul 13, 2019 (153)
78 ACPOP ss3740240013 Jul 13, 2019 (153)
79 ILLUMINA ss3744870785 Jul 13, 2019 (153)
80 EVA ss3752129174 Jul 13, 2019 (153)
81 ILLUMINA ss3772369708 Jul 13, 2019 (153)
82 PACBIO ss3787621567 Jul 13, 2019 (153)
83 PACBIO ss3792667315 Jul 13, 2019 (153)
84 PACBIO ss3797551399 Jul 13, 2019 (153)
85 KHV_HUMAN_GENOMES ss3817460911 Jul 13, 2019 (153)
86 EVA ss3833834584 Apr 27, 2020 (154)
87 EVA ss3840510006 Apr 27, 2020 (154)
88 EVA ss3845997929 Apr 27, 2020 (154)
89 SGDP_PRJ ss3881168399 Apr 27, 2020 (154)
90 KRGDB ss3930146503 Apr 27, 2020 (154)
91 KOGIC ss3974618484 Apr 27, 2020 (154)
92 TOPMED ss4965139662 Apr 26, 2021 (155)
93 TOMMO_GENOMICS ss5212515961 Apr 26, 2021 (155)
94 1000Genomes NC_000014.8 - 30208630 Oct 12, 2018 (152)
95 The Avon Longitudinal Study of Parents and Children NC_000014.8 - 30208630 Oct 12, 2018 (152)
96 Genetic variation in the Estonian population NC_000014.8 - 30208630 Oct 12, 2018 (152)
97 The Danish reference pan genome NC_000014.8 - 30208630 Apr 27, 2020 (154)
98 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 446560276 (NC_000014.9:29739423:G:A 1/139852)
Row 446560277 (NC_000014.9:29739423:G:T 69763/139776)

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

Submission ignored due to conflicting rows:
Row 446560276 (NC_000014.9:29739423:G:A 1/139852)
Row 446560277 (NC_000014.9:29739423:G:T 69763/139776)

- Apr 26, 2021 (155)
100 Genome of the Netherlands Release 5 NC_000014.8 - 30208630 Apr 27, 2020 (154)
101 HapMap NC_000014.9 - 29739424 Apr 27, 2020 (154)
102 KOREAN population from KRGDB NC_000014.8 - 30208630 Apr 27, 2020 (154)
103 Korean Genome Project NC_000014.9 - 29739424 Apr 27, 2020 (154)
104 Northern Sweden NC_000014.8 - 30208630 Jul 13, 2019 (153)
105 Qatari NC_000014.8 - 30208630 Apr 27, 2020 (154)
106 SGDP_PRJ NC_000014.8 - 30208630 Apr 27, 2020 (154)
107 Siberian NC_000014.8 - 30208630 Apr 27, 2020 (154)
108 8.3KJPN NC_000014.8 - 30208630 Apr 26, 2021 (155)
109 TopMed NC_000014.9 - 29739424 Apr 26, 2021 (155)
110 UK 10K study - Twins NC_000014.8 - 30208630 Oct 12, 2018 (152)
111 ALFA NC_000014.9 - 29739424 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).

Associated ID History Updated (Build)
rs61425317 May 26, 2008 (130)
rs386550493 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
37323897, ss3930146503 NC_000014.8:30208629:G:A NC_000014.9:29739423:G:A (self)
6472438932, ss3207027426 NC_000014.9:29739423:G:A NC_000014.9:29739423:G:A (self)
ss81645587, ss89894141, ss108211862, ss113091531, ss118395325, ss167757627, ss169036586, ss199876459, ss206957488, ss281940331, ss286812552, ss291692395, ss480360765, ss1694967928 NC_000014.7:29278380:G:T NC_000014.9:29739423:G:T (self)
63325179, 35175295, 24921193, 3535463, 15712295, 37323897, 13524878, 16394523, 33185379, 8838804, 70485268, 35175295, ss226485672, ss236479296, ss242926176, ss480372855, ss481142942, ss484977956, ss537015186, ss563997118, ss659660170, ss778474321, ss782935286, ss783898019, ss832190795, ss833930130, ss990976481, ss1079525627, ss1350369561, ss1427372205, ss1577146347, ss1631401128, ss1674395161, ss1752127816, ss1807850641, ss1934352593, ss1967924940, ss2027950685, ss2156322450, ss2364969768, ss2628464175, ss2633131257, ss2700738515, ss2925884741, ss3011941433, ss3350730797, ss3627184850, ss3631130518, ss3633070942, ss3633774141, ss3634570180, ss3635463742, ss3636259165, ss3637214892, ss3640277508, ss3679182945, ss3740240013, ss3744870785, ss3752129174, ss3772369708, ss3787621567, ss3792667315, ss3797551399, ss3833834584, ss3840510006, ss3881168399, ss3930146503, ss5212515961 NC_000014.8:30208629:G:T NC_000014.9:29739423:G:T (self)
1113061, 30996485, 113029883, 180685321, 6472438932, ss2200668609, ss3027798237, ss3207027427, ss3650171066, ss3696364925, ss3817460911, ss3845997929, ss3974618484, ss4965139662 NC_000014.9:29739423:G:T NC_000014.9:29739423:G:T (self)
ss12297820, ss21207949 NT_026437.10:10128668:G:T NC_000014.9:29739423:G:T (self)
ss2854951, ss6160335, ss6896430, ss23577880, ss43598593, ss70452589, ss96903707, ss103173036, ss133894617, ss143683281, ss160481886 NT_026437.12:11208629:G:T NC_000014.9:29739423: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 rs1959440

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.post596+ae089ad