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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.

rs13219424

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:128010939 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.244743 (64781/264690, TOPMED)
T=0.48563 (13720/28252, 14KJPN)
T=0.24361 (6248/25648, ALFA) (+ 15 more)
T=0.48878 (8192/16760, 8.3KJPN)
T=0.2583 (1654/6404, 1000G_30x)
T=0.2682 (1343/5008, 1000G)
T=0.4013 (1798/4480, Estonian)
T=0.3080 (1187/3854, ALSPAC)
T=0.3074 (1140/3708, TWINSUK)
T=0.4286 (1254/2926, KOREAN)
T=0.298 (297/998, GoNL)
T=0.350 (210/600, NorthernSweden)
C=0.382 (123/322, SGDP_PRJ)
T=0.204 (44/216, Qatari)
T=0.271 (58/214, Vietnamese)
T=0.009 (1/116, HapMap)
T=0.35 (14/40, GENOME_DK)
C=0.43 (12/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTPRK : Intron 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 25648 C=0.75639 A=0.00000, T=0.24361 0.594042 0.081254 0.324704 32
European Sub 20676 C=0.72427 A=0.00000, T=0.27573 0.54024 0.091701 0.36806 34
African Sub 2758 C=0.9877 A=0.0000, T=0.0123 0.976795 0.00145 0.021755 9
African Others Sub 116 C=0.991 A=0.000, T=0.009 0.982759 0.0 0.017241 0
African American Sub 2642 C=0.9875 A=0.0000, T=0.0125 0.976533 0.001514 0.021953 9
Asian Sub 66 C=0.85 A=0.00, T=0.15 0.787879 0.090909 0.121212 6
East Asian Sub 50 C=0.84 A=0.00, T=0.16 0.8 0.12 0.08 7
Other Asian Sub 16 C=0.88 A=0.00, T=0.12 0.75 0.0 0.25 0
Latin American 1 Sub 102 C=0.941 A=0.000, T=0.059 0.901961 0.019608 0.078431 3
Latin American 2 Sub 332 C=0.861 A=0.000, T=0.139 0.789157 0.066265 0.144578 14
South Asian Sub 76 C=0.91 A=0.00, T=0.09 0.894737 0.078947 0.026316 15
Other Sub 1638 C=0.7289 A=0.0000, T=0.2711 0.54823 0.090354 0.361416 4


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 C=0.755257 T=0.244743
14KJPN JAPANESE Study-wide 28252 C=0.51437 T=0.48563
Allele Frequency Aggregator Total Global 25648 C=0.75639 A=0.00000, T=0.24361
Allele Frequency Aggregator European Sub 20676 C=0.72427 A=0.00000, T=0.27573
Allele Frequency Aggregator African Sub 2758 C=0.9877 A=0.0000, T=0.0123
Allele Frequency Aggregator Other Sub 1638 C=0.7289 A=0.0000, T=0.2711
Allele Frequency Aggregator Latin American 2 Sub 332 C=0.861 A=0.000, T=0.139
Allele Frequency Aggregator Latin American 1 Sub 102 C=0.941 A=0.000, T=0.059
Allele Frequency Aggregator South Asian Sub 76 C=0.91 A=0.00, T=0.09
Allele Frequency Aggregator Asian Sub 66 C=0.85 A=0.00, T=0.15
8.3KJPN JAPANESE Study-wide 16760 C=0.51122 T=0.48878
1000Genomes_30x Global Study-wide 6404 C=0.7417 T=0.2583
1000Genomes_30x African Sub 1786 C=0.9614 T=0.0386
1000Genomes_30x Europe Sub 1266 C=0.6896 T=0.3104
1000Genomes_30x South Asian Sub 1202 C=0.7030 T=0.2970
1000Genomes_30x East Asian Sub 1170 C=0.6060 T=0.3940
1000Genomes_30x American Sub 980 C=0.618 T=0.382
1000Genomes Global Study-wide 5008 C=0.7318 T=0.2682
1000Genomes African Sub 1322 C=0.9576 T=0.0424
1000Genomes East Asian Sub 1008 C=0.5893 T=0.4107
1000Genomes Europe Sub 1006 C=0.6859 T=0.3141
1000Genomes South Asian Sub 978 C=0.703 T=0.297
1000Genomes American Sub 694 C=0.615 T=0.385
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5987 T=0.4013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.6920 T=0.3080
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.6926 T=0.3074
KOREAN population from KRGDB KOREAN Study-wide 2926 C=0.5714 A=0.0000, T=0.4286
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.702 T=0.298
Northern Sweden ACPOP Study-wide 600 C=0.650 T=0.350
SGDP_PRJ Global Study-wide 322 C=0.382 T=0.618
Qatari Global Study-wide 216 C=0.796 T=0.204
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.729 T=0.271
HapMap Global Study-wide 116 C=0.991 T=0.009
HapMap African Sub 116 C=0.991 T=0.009
The Danish reference pan genome Danish Study-wide 40 C=0.65 T=0.35
Siberian Global Study-wide 28 C=0.43 T=0.57
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 6 NC_000006.12:g.128010939C>A
GRCh38.p14 chr 6 NC_000006.12:g.128010939C>T
GRCh37.p13 chr 6 NC_000006.11:g.128332084C>A
GRCh37.p13 chr 6 NC_000006.11:g.128332084C>T
GRCh38.p14 chr 6 alt locus HSCHR6_1_CTG8 NT_187556.1:g.360272T>C
GRCh38.p14 chr 6 alt locus HSCHR6_1_CTG8 NT_187556.1:g.360272T>A
Gene: PTPRK, protein tyrosine phosphatase receptor type K (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PTPRK transcript variant 1 NM_001135648.3:c.2195-167…

NM_001135648.3:c.2195-1671G>T

N/A Intron Variant
PTPRK transcript variant 3 NM_001291981.2:c.2195-167…

NM_001291981.2:c.2195-1671G>T

N/A Intron Variant
PTPRK transcript variant 4 NM_001291982.2:c.2195-167…

NM_001291982.2:c.2195-1671G>T

N/A Intron Variant
PTPRK transcript variant 5 NM_001291983.2:c.1808-167…

NM_001291983.2:c.1808-1671G>T

N/A Intron Variant
PTPRK transcript variant 6 NM_001291984.2:c.2195-167…

NM_001291984.2:c.2195-1674G>T

N/A Intron Variant
PTPRK transcript variant 2 NM_002844.4:c.2195-1671G>T 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
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
GRCh38.p14 chr 6 NC_000006.12:g.128010939= NC_000006.12:g.128010939C>A NC_000006.12:g.128010939C>T
GRCh37.p13 chr 6 NC_000006.11:g.128332084= NC_000006.11:g.128332084C>A NC_000006.11:g.128332084C>T
GRCh38.p14 chr 6 alt locus HSCHR6_1_CTG8 NT_187556.1:g.360272T>C NT_187556.1:g.360272T>A NT_187556.1:g.360272=
PTPRK transcript variant 1 NM_001135648.1:c.2195-1671= NM_001135648.1:c.2195-1671G>T NM_001135648.1:c.2195-1671G>A
PTPRK transcript variant 1 NM_001135648.3:c.2195-1671= NM_001135648.3:c.2195-1671G>T NM_001135648.3:c.2195-1671G>A
PTPRK transcript variant 3 NM_001291981.2:c.2195-1671= NM_001291981.2:c.2195-1671G>T NM_001291981.2:c.2195-1671G>A
PTPRK transcript variant 4 NM_001291982.2:c.2195-1671= NM_001291982.2:c.2195-1671G>T NM_001291982.2:c.2195-1671G>A
PTPRK transcript variant 5 NM_001291983.2:c.1808-1671= NM_001291983.2:c.1808-1671G>T NM_001291983.2:c.1808-1671G>A
PTPRK transcript variant 6 NM_001291984.2:c.2195-1674= NM_001291984.2:c.2195-1674G>T NM_001291984.2:c.2195-1674G>A
PTPRK transcript variant 2 NM_002844.3:c.2195-1671= NM_002844.3:c.2195-1671G>T NM_002844.3:c.2195-1671G>A
PTPRK transcript variant 2 NM_002844.4:c.2195-1671= NM_002844.4:c.2195-1671G>T NM_002844.4:c.2195-1671G>A
PTPRK transcript variant X1 XM_005267081.1:c.2195-1671= XM_005267081.1:c.2195-1671G>T XM_005267081.1:c.2195-1671G>A
PTPRK transcript variant X2 XM_005267082.1:c.2195-1671= XM_005267082.1:c.2195-1671G>T XM_005267082.1:c.2195-1671G>A
PTPRK transcript variant X3 XM_005267083.1:c.2195-1671= XM_005267083.1:c.2195-1671G>T XM_005267083.1:c.2195-1671G>A
PTPRK transcript variant X4 XM_005267084.1:c.2195-1671= XM_005267084.1:c.2195-1671G>T XM_005267084.1:c.2195-1671G>A
PTPRK transcript variant X5 XM_005267085.1:c.2195-1674= XM_005267085.1:c.2195-1674G>T XM_005267085.1:c.2195-1674G>A
PTPRK transcript variant X6 XM_005267086.1:c.2195-1671= XM_005267086.1:c.2195-1671G>T XM_005267086.1:c.2195-1671G>A
PTPRK transcript variant X7 XM_005267087.1:c.2195-1671= XM_005267087.1:c.2195-1671G>T XM_005267087.1:c.2195-1671G>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#.

72 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss22509596 Apr 05, 2004 (121)
2 ABI ss44756925 Mar 15, 2006 (126)
3 HUMANGENOME_JCVI ss98540417 Feb 05, 2009 (130)
4 BGI ss104358519 Dec 01, 2009 (131)
5 ENSEMBL ss144299630 Dec 01, 2009 (131)
6 BUSHMAN ss202408602 Jul 04, 2010 (132)
7 BCM-HGSC-SUB ss207621347 Jul 04, 2010 (132)
8 1000GENOMES ss222668296 Jul 14, 2010 (132)
9 1000GENOMES ss233679349 Jul 15, 2010 (132)
10 1000GENOMES ss240695326 Jul 15, 2010 (132)
11 BL ss254705670 May 09, 2011 (134)
12 GMI ss279018905 May 04, 2012 (137)
13 PJP ss293722290 May 09, 2011 (134)
14 ILLUMINA ss483521664 May 04, 2012 (137)
15 ILLUMINA ss485143822 May 04, 2012 (137)
16 ILLUMINA ss535729349 Sep 08, 2015 (146)
17 SSMP ss653747371 Apr 25, 2013 (138)
18 ILLUMINA ss780309004 Sep 08, 2015 (146)
19 ILLUMINA ss782204371 Sep 08, 2015 (146)
20 ILLUMINA ss835795903 Sep 08, 2015 (146)
21 EVA-GONL ss983489739 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1074026072 Aug 21, 2014 (142)
23 1000GENOMES ss1322234039 Aug 21, 2014 (142)
24 EVA_GENOME_DK ss1581894032 Apr 01, 2015 (144)
25 EVA_DECODE ss1593057417 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1616673567 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1659667600 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1926733340 Feb 12, 2016 (147)
29 GENOMED ss1970524092 Jul 19, 2016 (147)
30 JJLAB ss2024022679 Sep 14, 2016 (149)
31 ILLUMINA ss2094965223 Dec 20, 2016 (150)
32 ILLUMINA ss2095189860 Dec 20, 2016 (150)
33 USC_VALOUEV ss2152216963 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2288307239 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2626506409 Nov 08, 2017 (151)
36 ILLUMINA ss2634509608 Nov 08, 2017 (151)
37 GRF ss2707848610 Nov 08, 2017 (151)
38 SWEGEN ss2999937334 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3025805485 Nov 08, 2017 (151)
40 CSHL ss3347224787 Nov 08, 2017 (151)
41 ILLUMINA ss3629652706 Oct 12, 2018 (152)
42 ILLUMINA ss3632422915 Oct 12, 2018 (152)
43 ILLUMINA ss3642517817 Oct 12, 2018 (152)
44 URBANLAB ss3648470596 Oct 12, 2018 (152)
45 ILLUMINA ss3653187554 Oct 12, 2018 (152)
46 EGCUT_WGS ss3667850858 Jul 13, 2019 (153)
47 EVA_DECODE ss3718258401 Jul 13, 2019 (153)
48 ACPOP ss3733974871 Jul 13, 2019 (153)
49 EVA ss3765659387 Jul 13, 2019 (153)
50 PACBIO ss3785618874 Jul 13, 2019 (153)
51 PACBIO ss3790947423 Jul 13, 2019 (153)
52 PACBIO ss3795826681 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3808815222 Jul 13, 2019 (153)
54 EVA ss3830187902 Apr 26, 2020 (154)
55 SGDP_PRJ ss3865687497 Apr 26, 2020 (154)
56 KRGDB ss3912641725 Apr 26, 2020 (154)
57 VINODS ss4025303934 Apr 26, 2021 (155)
58 TOPMED ss4721547125 Apr 26, 2021 (155)
59 TOMMO_GENOMICS ss5179892442 Apr 26, 2021 (155)
60 1000G_HIGH_COVERAGE ss5270316235 Oct 13, 2022 (156)
61 EVA ss5315189738 Oct 13, 2022 (156)
62 HUGCELL_USP ss5467760053 Oct 13, 2022 (156)
63 EVA ss5508706863 Oct 13, 2022 (156)
64 1000G_HIGH_COVERAGE ss5557245667 Oct 13, 2022 (156)
65 SANFORD_IMAGENETICS ss5641472434 Oct 13, 2022 (156)
66 TOMMO_GENOMICS ss5718766675 Oct 13, 2022 (156)
67 YY_MCH ss5807951848 Oct 13, 2022 (156)
68 EVA ss5842974963 Oct 13, 2022 (156)
69 EVA ss5855579224 Oct 13, 2022 (156)
70 EVA ss5885915596 Oct 13, 2022 (156)
71 EVA ss5970129957 Oct 13, 2022 (156)
72 EVA ss5970129958 Oct 13, 2022 (156)
73 1000Genomes NC_000006.11 - 128332084 Oct 12, 2018 (152)
74 1000Genomes_30x NC_000006.12 - 128010939 Oct 13, 2022 (156)
75 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 128332084 Oct 12, 2018 (152)
76 Genetic variation in the Estonian population NC_000006.11 - 128332084 Oct 12, 2018 (152)
77 The Danish reference pan genome NC_000006.11 - 128332084 Apr 26, 2020 (154)
78 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 240846040 (NC_000006.12:128010938:C:A 2/138856)
Row 240846041 (NC_000006.12:128010938:C:T 34659/138800)

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

Submission ignored due to conflicting rows:
Row 240846040 (NC_000006.12:128010938:C:A 2/138856)
Row 240846041 (NC_000006.12:128010938:C:T 34659/138800)

- Apr 26, 2021 (155)
80 Genome of the Netherlands Release 5 NC_000006.11 - 128332084 Apr 26, 2020 (154)
81 HapMap NC_000006.12 - 128010939 Apr 26, 2020 (154)
82 KOREAN population from KRGDB NC_000006.11 - 128332084 Apr 26, 2020 (154)
83 Northern Sweden NC_000006.11 - 128332084 Jul 13, 2019 (153)
84 Qatari NC_000006.11 - 128332084 Apr 26, 2020 (154)
85 SGDP_PRJ NC_000006.11 - 128332084 Apr 26, 2020 (154)
86 Siberian NC_000006.11 - 128332084 Apr 26, 2020 (154)
87 8.3KJPN NC_000006.11 - 128332084 Apr 26, 2021 (155)
88 14KJPN NC_000006.12 - 128010939 Oct 13, 2022 (156)
89 TopMed NC_000006.12 - 128010939 Apr 26, 2021 (155)
90 UK 10K study - Twins NC_000006.11 - 128332084 Oct 12, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000006.11 - 128332084 Jul 13, 2019 (153)
92 ALFA NC_000006.12 - 128010939 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
19819119, ss3912641725 NC_000006.11:128332083:C:A NC_000006.12:128010938:C:A (self)
2892820083 NC_000006.12:128010938:C:A NC_000006.12:128010938:C:A (self)
ss202408602, ss207621347, ss254705670, ss279018905, ss293722290, ss485143822, ss1593057417, ss2094965223 NC_000006.10:128373776:C:T NC_000006.12:128010938:C:T (self)
34101609, 19002935, 13589106, 8058971, 8464672, 19819119, 7259736, 8775270, 17704477, 4733317, 37861749, 19002935, 4231136, ss222668296, ss233679349, ss240695326, ss483521664, ss535729349, ss653747371, ss780309004, ss782204371, ss835795903, ss983489739, ss1074026072, ss1322234039, ss1581894032, ss1616673567, ss1659667600, ss1926733340, ss1970524092, ss2024022679, ss2095189860, ss2152216963, ss2626506409, ss2634509608, ss2707848610, ss2999937334, ss3347224787, ss3629652706, ss3632422915, ss3642517817, ss3653187554, ss3667850858, ss3733974871, ss3765659387, ss3785618874, ss3790947423, ss3795826681, ss3830187902, ss3865687497, ss3912641725, ss5179892442, ss5315189738, ss5508706863, ss5641472434, ss5842974963, ss5970129957, ss5970129958 NC_000006.11:128332083:C:T NC_000006.12:128010938:C:T (self)
44771602, 3245877, 52603779, 558924683, 2892820083, ss2288307239, ss3025805485, ss3648470596, ss3718258401, ss3808815222, ss4721547125, ss5270316235, ss5467760053, ss5557245667, ss5718766675, ss5807951848, ss5855579224, ss5885915596 NC_000006.12:128010938:C:T NC_000006.12:128010938:C:T (self)
ss22509596 NT_025741.13:32436512:C:T NC_000006.12:128010938:C:T (self)
ss44756925, ss98540417, ss104358519, ss144299630 NT_025741.15:32501540:C:T NC_000006.12:128010938:C:T (self)
ss4025303934 NT_187556.1:360271:T:T NC_000006.12:128010938: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.

No publications for rs13219424

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.post820+afb47a3d