Skip to main page content
Accesskeys

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 Aliases 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.

rs212146

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr21:10592359 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00000 (1/251038, GnomAD_exome)
A=0.00000 (0/125568, TOPMED)
A=0.00000 (0/121328, ExAC) (+ 2 more)
A=0.0000 (0/31416, GnomAD)
A=0.000 (0/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TPTE : Stop Gained
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.p12 chr 21 NC_000021.9:g.10592359A>C
GRCh38.p12 chr 21 NC_000021.9:g.10592359A>G
GRCh38.p12 chr 21 NC_000021.9:g.10592359A>T
GRCh37.p13 chr 21 NC_000021.8:g.10920098T>G
GRCh37.p13 chr 21 NC_000021.8:g.10920098T>C
GRCh37.p13 chr 21 NC_000021.8:g.10920098T>A
TPTE RefSeqGene NG_034032.1:g.75846G>A
TPTE RefSeqGene NG_034032.1:g.75846G>C
TPTE RefSeqGene NG_034032.1:g.75846G>T
Gene: TPTE, transmembrane phosphatase with tensin homology (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TPTE transcript variant 4 NM_001290224.1:c.742G>A E [GAA] > K [AAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform delta NP_001277153.1:p.Glu248Lys E (Glu) > K (Lys) Missense Variant
TPTE transcript variant 4 NM_001290224.1:c.742G>C E [GAA] > Q [CAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform delta NP_001277153.1:p.Glu248Gln E (Glu) > Q (Gln) Missense Variant
TPTE transcript variant 4 NM_001290224.1:c.742G>T E [GAA] > * [TAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform delta NP_001277153.1:p.Glu248Ter E (Glu) > * (Ter) Stop Gained
TPTE transcript variant 1 NM_199261.3:c.1156G>A E [GAA] > K [AAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform alpha NP_954870.2:p.Glu386Lys E (Glu) > K (Lys) Missense Variant
TPTE transcript variant 1 NM_199261.3:c.1156G>C E [GAA] > Q [CAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform alpha NP_954870.2:p.Glu386Gln E (Glu) > Q (Gln) Missense Variant
TPTE transcript variant 1 NM_199261.3:c.1156G>T E [GAA] > * [TAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform alpha NP_954870.2:p.Glu386Ter E (Glu) > * (Ter) Stop Gained
TPTE transcript variant 3 NM_199260.3:c.1042G>A E [GAA] > K [AAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform gamma NP_954869.1:p.Glu348Lys E (Glu) > K (Lys) Missense Variant
TPTE transcript variant 3 NM_199260.3:c.1042G>C E [GAA] > Q [CAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform gamma NP_954869.1:p.Glu348Gln E (Glu) > Q (Gln) Missense Variant
TPTE transcript variant 3 NM_199260.3:c.1042G>T E [GAA] > * [TAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform gamma NP_954869.1:p.Glu348Ter E (Glu) > * (Ter) Stop Gained
TPTE transcript variant 2 NM_199259.3:c.1102G>A E [GAA] > K [AAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform beta NP_954868.1:p.Glu368Lys E (Glu) > K (Lys) Missense Variant
TPTE transcript variant 2 NM_199259.3:c.1102G>C E [GAA] > Q [CAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform beta NP_954868.1:p.Glu368Gln E (Glu) > Q (Gln) Missense Variant
TPTE transcript variant 2 NM_199259.3:c.1102G>T E [GAA] > * [TAA] Coding Sequence Variant
putative tyrosine-protein phosphatase TPTE isoform beta NP_954868.1:p.Glu368Ter E (Glu) > * (Ter) Stop Gained
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

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 251038 A=0.00000 G=1.00000
gnomAD - Exomes European Sub 135064 A=0.00000 G=1.00000
gnomAD - Exomes Asian Sub 49000 A=0.0000 G=1.0000
gnomAD - Exomes American Sub 34566 A=0.0000 G=1.0000
gnomAD - Exomes African Sub 16208 A=0.0000 G=1.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 A=0.0000 G=1.0000
gnomAD - Exomes Other Sub 6120 A=0.000 G=1.000
TopMed Global Study-wide 125568 A=0.00000 G=1.00000
ExAC Global Study-wide 121328 A=0.00000 G=1.00000
ExAC Europe Sub 73336 A=0.0000 G=1.0000
ExAC Asian Sub 25160 A=0.0000 G=1.0000
ExAC American Sub 11560 A=0.0000 G=1.0000
ExAC African Sub 10364 A=0.0000 G=1.0000
ExAC Other Sub 908 A=0.00 G=1.00
gnomAD - Genomes Global Study-wide 31416 A=0.0000 G=1.0000
gnomAD - Genomes European Sub 18912 A=0.0000 G=1.0000
gnomAD - Genomes African Sub 8718 A=0.000 G=1.000
gnomAD - Genomes East Asian Sub 1560 A=0.000 G=1.000
gnomAD - Genomes Other Sub 1088 A=0.000 G=1.000
gnomAD - Genomes American Sub 848 A=0.00 G=1.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.00 G=1.00
1000Genomes Global Study-wide 5008 A=0.000 G=1.000
1000Genomes African Sub 1322 A=0.000 G=1.000
1000Genomes East Asian Sub 1008 A=0.000 G=1.000
1000Genomes Europe Sub 1006 A=0.000 G=1.000
1000Genomes South Asian Sub 978 A=0.00 G=1.00
1000Genomes American Sub 694 A=0.00 G=1.00
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= C G T Note
GRCh38.p12 chr 21 NC_000021.9:g...

NC_000021.9:g.10592359=

NC_000021.9:g...

NC_000021.9:g.10592359A>C

NC_000021.9:g...

NC_000021.9:g.10592359A>G

NC_000021.9:g...

NC_000021.9:g.10592359A>T

GRCh37.p13 chr 21 NC_000021.8:g...

NC_000021.8:g.10920098=

NC_000021.8:g...

NC_000021.8:g.10920098T>G

NC_000021.8:g...

NC_000021.8:g.10920098T>C

NC_000021.8:g...

NC_000021.8:g.10920098T>A

TPTE RefSeqGene NG_034032.1:g...

NG_034032.1:g.75846G>A

NG_034032.1:g...

NG_034032.1:g.75846G>C

NG_034032.1:g...

NG_034032.1:g.75846=

NG_034032.1:g...

NG_034032.1:g.75846G>T

TPTE transcript variant 1 NM_199261.3:c...

NM_199261.3:c.1156G>A

NM_199261.3:c...

NM_199261.3:c.1156G>C

NM_199261.3:c...

NM_199261.3:c.1156=

NM_199261.3:c...

NM_199261.3:c.1156G>T

TPTE transcript variant 1 NM_199261.2:c...

NM_199261.2:c.1156G>A

NM_199261.2:c...

NM_199261.2:c.1156G>C

NM_199261.2:c...

NM_199261.2:c.1156=

NM_199261.2:c...

NM_199261.2:c.1156G>T

TPTE transcript variant 2 NM_199259.3:c...

NM_199259.3:c.1102G>A

NM_199259.3:c...

NM_199259.3:c.1102G>C

NM_199259.3:c...

NM_199259.3:c.1102=

NM_199259.3:c...

NM_199259.3:c.1102G>T

TPTE transcript variant 2 NM_199259.2:c...

NM_199259.2:c.1102G>A

NM_199259.2:c...

NM_199259.2:c.1102G>C

NM_199259.2:c...

NM_199259.2:c.1102=

NM_199259.2:c...

NM_199259.2:c.1102G>T

TPTE transcript variant 3 NM_199260.3:c...

NM_199260.3:c.1042G>A

NM_199260.3:c...

NM_199260.3:c.1042G>C

NM_199260.3:c...

NM_199260.3:c.1042=

NM_199260.3:c...

NM_199260.3:c.1042G>T

TPTE transcript variant 3 NM_199260.2:c...

NM_199260.2:c.1042G>A

NM_199260.2:c...

NM_199260.2:c.1042G>C

NM_199260.2:c...

NM_199260.2:c.1042=

NM_199260.2:c...

NM_199260.2:c.1042G>T

TPTE transcript variant 4 NM_001290224....

NM_001290224.1:c.742G>A

NM_001290224....

NM_001290224.1:c.742G>C

NM_001290224....

NM_001290224.1:c.742=

NM_001290224....

NM_001290224.1:c.742G>T

putative tyrosine-protein phosphatase TPTE isoform alpha NP_954870.2:p...

NP_954870.2:p.Glu386Lys

NP_954870.2:p...

NP_954870.2:p.Glu386Gln

NP_954870.2:p...

NP_954870.2:p.Glu386=

NP_954870.2:p...

NP_954870.2:p.Glu386Ter

putative tyrosine-protein phosphatase TPTE isoform beta NP_954868.1:p...

NP_954868.1:p.Glu368Lys

NP_954868.1:p...

NP_954868.1:p.Glu368Gln

NP_954868.1:p...

NP_954868.1:p.Glu368=

NP_954868.1:p...

NP_954868.1:p.Glu368Ter

putative tyrosine-protein phosphatase TPTE isoform gamma NP_954869.1:p...

NP_954869.1:p.Glu348Lys

NP_954869.1:p...

NP_954869.1:p.Glu348Gln

NP_954869.1:p...

NP_954869.1:p.Glu348=

NP_954869.1:p...

NP_954869.1:p.Glu348Ter

putative tyrosine-protein phosphatase TPTE isoform delta NP_001277153....

NP_001277153.1:p.Glu248Lys

NP_001277153....

NP_001277153.1:p.Glu248Gln

NP_001277153....

NP_001277153.1:p.Glu248=

NP_001277153....

NP_001277153.1:p.Glu248Ter

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#.

74 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss277229 Jul 12, 2000 (79)
2 SC_JCM ss634514 Jul 16, 2000 (80)
3 WI_SSAHASNP ss6791786 Feb 20, 2003 (111)
4 BCM_SSAHASNP ss10989237 Jul 11, 2003 (116)
5 WI_SSAHASNP ss12514252 Jul 11, 2003 (116)
6 WUGSC_SSAHASNP ss14437839 Dec 05, 2003 (119)
7 SC_SNP ss14743668 Dec 05, 2003 (119)
8 CSHL-HAPMAP ss17707113 Feb 27, 2004 (120)
9 CSHL-HAPMAP ss19487473 Feb 27, 2004 (120)
10 SEQUENOM ss24803995 Sep 20, 2004 (123)
11 MGC_GENOME_DIFF ss28509837 Sep 24, 2004 (126)
12 ILLUMINA ss74870937 Dec 07, 2007 (129)
13 HGSV ss77704531 Dec 07, 2007 (129)
14 HGSV ss83884759 Dec 14, 2007 (130)
15 HGSV ss84735011 Dec 14, 2007 (130)
16 HGSV ss85752497 Dec 14, 2007 (130)
17 HGSV ss85954431 Dec 14, 2007 (130)
18 BCMHGSC_JDW ss91762368 Mar 24, 2008 (129)
19 HUMANGENOME_JCVI ss96133581 Feb 04, 2009 (130)
20 BGI ss106199825 Feb 04, 2009 (130)
21 ILLUMINA-UK ss117448359 Feb 14, 2009 (130)
22 ENSEMBL ss135582870 Dec 01, 2009 (131)
23 ENSEMBL ss138278310 Dec 01, 2009 (131)
24 GMI ss156646352 Dec 01, 2009 (131)
25 SEATTLESEQ ss159743032 Dec 01, 2009 (131)
26 ILLUMINA ss161072657 Dec 01, 2009 (131)
27 ILLUMINA ss173126499 Jul 04, 2010 (132)
28 BUSHMAN ss203951078 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss208804916 Jul 04, 2010 (132)
30 BL ss255832077 May 09, 2011 (134)
31 GMI ss283453865 May 04, 2012 (137)
32 GMI ss287490344 Apr 25, 2013 (138)
33 PJP ss292668991 May 09, 2011 (134)
34 1000GENOMES ss340882289 May 09, 2011 (134)
35 NHLBI-ESP ss342529221 May 09, 2011 (134)
36 ILLUMINA ss479186154 Sep 08, 2015 (146)
37 1000GENOMES ss491182398 May 04, 2012 (137)
38 EXOME_CHIP ss491564284 May 04, 2012 (137)
39 CLINSEQ_SNP ss491813947 May 04, 2012 (137)
40 ILLUMINA ss537041442 Sep 08, 2015 (146)
41 TISHKOFF ss566372258 Apr 25, 2013 (138)
42 SSMP ss662269436 Apr 25, 2013 (138)
43 JMKIDD_LAB ss1067600791 Aug 21, 2014 (142)
44 1000GENOMES ss1365541089 Aug 21, 2014 (142)
45 DDI ss1429117114 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1579581883 Apr 01, 2015 (144)
47 EVA_FINRISK ss1584124551 Apr 01, 2015 (144)
48 EVA_EXAC ss1694105725 Apr 01, 2015 (144)
49 EVA_MGP ss1711548736 Apr 01, 2015 (144)
50 EVA_SVP ss1713709084 Apr 01, 2015 (144)
51 HAMMER_LAB ss1809591923 Sep 08, 2015 (146)
52 WEILL_CORNELL_DGM ss1938461333 Feb 12, 2016 (147)
53 GENOMED ss1969174564 Jul 19, 2016 (147)
54 USC_VALOUEV ss2158593931 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2629496316 Nov 08, 2017 (151)
56 GRF ss2704307305 Nov 08, 2017 (151)
57 GNOMAD ss2744773611 Nov 08, 2017 (151)
58 GNOMAD ss2750436147 Nov 08, 2017 (151)
59 GNOMAD ss2969680147 Nov 08, 2017 (151)
60 SWEGEN ss3018560320 Nov 08, 2017 (151)
61 CSHL ss3352619068 Nov 08, 2017 (151)
62 TOPMED ss3365917828 Nov 08, 2017 (151)
63 ILLUMINA ss3628439692 Oct 12, 2018 (152)
64 ILLUMINA ss3636540653 Oct 12, 2018 (152)
65 ILLUMINA ss3638357839 Oct 12, 2018 (152)
66 ILLUMINA ss3643319734 Oct 12, 2018 (152)
67 OMUKHERJEE_ADBS ss3646554019 Oct 12, 2018 (152)
68 URBANLAB ss3651069767 Oct 12, 2018 (152)
69 EVA_DECODE ss3707353777 Jul 13, 2019 (153)
70 EVA ss3758880825 Jul 13, 2019 (153)
71 PACBIO ss3788704722 Jul 13, 2019 (153)
72 PACBIO ss3793587296 Jul 13, 2019 (153)
73 PACBIO ss3798474029 Jul 13, 2019 (153)
74 KHV_HUMAN_GENOMES ss3822035756 Jul 13, 2019 (153)
75 1000Genomes NC_000021.8 - 10920098 Oct 12, 2018 (152)
76 ExAC NC_000021.8 - 10920098 Oct 12, 2018 (152)
77 gnomAD - Genomes NC_000021.8 - 10920098 Jul 13, 2019 (153)
78 gnomAD - Exomes NC_000021.8 - 10920098 Jul 13, 2019 (153)
79 TopMed NC_000021.9 - 10592359 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).

Associated ID History Updated (Build)
rs17855535 Mar 10, 2006 (126)
rs57682955 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2744773611 NC_000021.8:10920097:T:G NC_000021.9:10592358:A:C (self)
ss24803995 NT_029490.4:222201:T:G NC_000021.9:10592358:A:C (self)
ss77704531, ss83884759, ss84735011, ss85752497, ss85954431, ss91762368, ss117448359, ss203951078, ss208804916, ss255832077, ss283453865, ss287490344, ss292668991, ss491813947, ss1713709084, ss3643319734 NC_000021.7:9941968:T:C NC_000021.9:10592358:A:G (self)
79030760, 5668189, 215642090, 14097343, ss340882289, ss342529221, ss479186154, ss491182398, ss491564284, ss537041442, ss566372258, ss662269436, ss1067600791, ss1365541089, ss1429117114, ss1579581883, ss1584124551, ss1694105725, ss1711548736, ss1809591923, ss1938461333, ss1969174564, ss2158593931, ss2629496316, ss2704307305, ss2744773611, ss2750436147, ss2969680147, ss3018560320, ss3352619068, ss3628439692, ss3636540653, ss3638357839, ss3646554019, ss3758880825, ss3788704722, ss3793587296, ss3798474029 NC_000021.8:10920097:T:C NC_000021.9:10592358:A:G (self)
231248373, ss3365917828, ss3651069767, ss3707353777, ss3822035756 NC_000021.9:10592358:A:G NC_000021.9:10592358:A:G (self)
ss6791786, ss10989237, ss12514252, ss14437839, ss14743668, ss17707113, ss19487473 NT_029490.3:13781:T:C NC_000021.9:10592358:A:G (self)
ss277229, ss634514, ss28509837, ss74870937, ss96133581, ss106199825, ss135582870, ss138278310, ss156646352, ss159743032, ss161072657, ss173126499 NT_029490.4:222201:T:C NC_000021.9:10592358:A:G (self)
ss24803995 NT_029490.4:222201:T:A NC_000021.9:10592358: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.

No publications for rs212146

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.post308+0fe9b3b