Skip to main page content
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.

rs14414

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:194403895 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.376463 (99646/264690, TOPMED)
T=0.364034 (49920/137130, GnomAD)
T=0.25703 (7692/29926, ALFA) (+ 13 more)
T=0.30561 (5122/16760, 8.3KJPN)
T=0.4119 (2063/5008, 1000G)
T=0.1775 (795/4480, Estonian)
T=0.2073 (799/3854, ALSPAC)
T=0.2087 (774/3708, TWINSUK)
T=0.3008 (880/2926, KOREAN)
T=0.172 (172/998, GoNL)
T=0.277 (166/600, NorthernSweden)
T=0.058 (31/534, MGP)
C=0.367 (113/308, SGDP_PRJ)
T=0.292 (63/216, Qatari)
T=0.25 (10/40, GENOME_DK)
C=0.46 (11/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATP13A3 : Non Coding Transcript 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 3 NC_000003.12:g.194403895C>A
GRCh38.p13 chr 3 NC_000003.12:g.194403895C>T
GRCh37.p13 chr 3 NC_000003.11:g.194124624C>A
GRCh37.p13 chr 3 NC_000003.11:g.194124624C>T
Gene: ATP13A3, ATPase 13A3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATP13A3 transcript variant 2 NM_001367549.1:c.*2024= N/A 3 Prime UTR Variant
ATP13A3 transcript variant 3 NM_001374836.1:c.*2024= N/A 3 Prime UTR Variant
ATP13A3 transcript variant 1 NM_024524.4:c.*2024= N/A 3 Prime UTR Variant
ATP13A3 transcript variant 5 NR_164667.1:n.6277G>T N/A Non Coding Transcript Variant
ATP13A3 transcript variant 5 NR_164667.1:n.6277G>A N/A Non Coding Transcript Variant
ATP13A3 transcript variant 4 NR_164666.1:n. N/A Genic Downstream Transcript Variant
ATP13A3 transcript variant X3 XM_011513121.1:c.*2024= N/A 3 Prime UTR Variant
ATP13A3 transcript variant X2 XM_005269357.3:c.*2024= N/A 3 Prime UTR Variant
ATP13A3 transcript variant X5 XM_011513123.2:c.*2024= N/A 3 Prime UTR Variant
ATP13A3 transcript variant X6 XM_011513124.3:c. N/A Genic Downstream Transcript 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
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 29926 C=0.74297 A=0.00000, T=0.25703
European Sub 24324 C=0.79333 A=0.00000, T=0.20667
African Sub 2684 C=0.3260 A=0.0000, T=0.6740
African Others Sub 102 C=0.176 A=0.000, T=0.824
African American Sub 2582 C=0.3319 A=0.0000, T=0.6681
Asian Sub 126 C=0.722 A=0.000, T=0.278
East Asian Sub 98 C=0.69 A=0.00, T=0.31
Other Asian Sub 28 C=0.82 A=0.00, T=0.18
Latin American 1 Sub 164 C=0.549 A=0.000, T=0.451
Latin American 2 Sub 684 C=0.743 A=0.000, T=0.257
South Asian Sub 114 C=0.579 A=0.000, T=0.421
Other Sub 1830 C=0.7142 A=0.0000, T=0.2858


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=0.623537 T=0.376463
gnomAD - Genomes Global Study-wide 137130 C=0.635966 T=0.364034
gnomAD - Genomes European Sub 74294 C=0.78689 T=0.21311
gnomAD - Genomes African Sub 41234 C=0.31930 T=0.68070
gnomAD - Genomes American Sub 13138 C=0.73413 T=0.26587
gnomAD - Genomes Ashkenazi Jewish Sub 3298 C=0.7277 T=0.2723
gnomAD - Genomes East Asian Sub 3082 C=0.7161 T=0.2839
gnomAD - Genomes Other Sub 2084 C=0.6387 T=0.3613
8.3KJPN JAPANESE Study-wide 16760 C=0.69439 T=0.30561
1000Genomes Global Study-wide 5008 C=0.5881 T=0.4119
1000Genomes African Sub 1322 C=0.2375 T=0.7625
1000Genomes East Asian Sub 1008 C=0.7272 T=0.2728
1000Genomes Europe Sub 1006 C=0.7932 T=0.2068
1000Genomes South Asian Sub 978 C=0.601 T=0.399
1000Genomes American Sub 694 C=0.738 T=0.262
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8225 T=0.1775
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7927 T=0.2073
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7913 T=0.2087
KOREAN population from KRGDB KOREAN Study-wide 2926 C=0.6992 T=0.3008
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.828 T=0.172
Northern Sweden ACPOP Study-wide 600 C=0.723 T=0.277
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.942 T=0.058
SGDP_PRJ Global Study-wide 308 C=0.367 T=0.633
Qatari Global Study-wide 216 C=0.708 T=0.292
The Danish reference pan genome Danish Study-wide 40 C=0.75 T=0.25
Siberian Global Study-wide 24 C=0.46 T=0.54
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.p13 chr 3 NC_000003.12:g.194403895= NC_000003.12:g.194403895C>A NC_000003.12:g.194403895C>T
GRCh37.p13 chr 3 NC_000003.11:g.194124624= NC_000003.11:g.194124624C>A NC_000003.11:g.194124624C>T
ATP13A3 transcript variant 1 NM_024524.4:c.*2024= NM_024524.4:c.*2024G>T NM_024524.4:c.*2024G>A
ATP13A3 transcript variant 1 NM_024524.3:c.*2024= NM_024524.3:c.*2024G>T NM_024524.3:c.*2024G>A
ATP13A3 transcript variant X2 XM_005269357.3:c.*2024= XM_005269357.3:c.*2024G>T XM_005269357.3:c.*2024G>A
ATP13A3 transcript variant X1 XM_005269357.1:c.*2024= XM_005269357.1:c.*2024G>T XM_005269357.1:c.*2024G>A
ATP13A3 transcript variant X5 XM_011513123.2:c.*2024= XM_011513123.2:c.*2024G>T XM_011513123.2:c.*2024G>A
ATP13A3 transcript variant 2 NM_001367549.1:c.*2024= NM_001367549.1:c.*2024G>T NM_001367549.1:c.*2024G>A
ATP13A3 transcript variant 5 NR_164667.1:n.6277= NR_164667.1:n.6277G>T NR_164667.1:n.6277G>A
ATP13A3 transcript variant 3 NM_001374836.1:c.*2024= NM_001374836.1:c.*2024G>T NM_001374836.1:c.*2024G>A
ATP13A3 transcript variant X3 XM_011513121.1:c.*2024= XM_011513121.1:c.*2024G>T XM_011513121.1:c.*2024G>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#.

74 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss16795 Sep 19, 2000 (52)
2 LEE ss1508758 Oct 04, 2000 (86)
3 LEE ss4403185 May 29, 2002 (106)
4 YUSUKE ss4958260 Aug 28, 2002 (108)
5 CSHL-HAPMAP ss20185326 Feb 27, 2004 (120)
6 SSAHASNP ss22027313 Apr 05, 2004 (121)
7 ABI ss44382960 Mar 14, 2006 (126)
8 HGSV ss78855897 Dec 06, 2007 (129)
9 HUMANGENOME_JCVI ss96088636 Feb 04, 2009 (130)
10 1000GENOMES ss111600795 Jan 25, 2009 (130)
11 ILLUMINA-UK ss117441690 Feb 14, 2009 (130)
12 ENSEMBL ss133183715 Dec 01, 2009 (131)
13 GMI ss156689392 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss162951791 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss165378272 Jul 04, 2010 (132)
16 BUSHMAN ss203687679 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss206135599 Jul 04, 2010 (132)
18 1000GENOMES ss220671419 Jul 14, 2010 (132)
19 1000GENOMES ss232208483 Jul 14, 2010 (132)
20 1000GENOMES ss239541278 Jul 15, 2010 (132)
21 GMI ss277519337 May 04, 2012 (137)
22 GMI ss284821452 Apr 25, 2013 (138)
23 PJP ss293011366 May 09, 2011 (134)
24 ILLUMINA ss484316589 May 04, 2012 (137)
25 ILLUMINA ss484544834 May 04, 2012 (137)
26 ILLUMINA ss536500275 Sep 08, 2015 (146)
27 SSMP ss650972649 Apr 25, 2013 (138)
28 ILLUMINA ss779531607 Sep 08, 2015 (146)
29 ILLUMINA ss782604493 Sep 08, 2015 (146)
30 ILLUMINA ss835002174 Sep 08, 2015 (146)
31 EVA-GONL ss979626638 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1071185431 Aug 21, 2014 (142)
33 1000GENOMES ss1307913714 Aug 21, 2014 (142)
34 DDI ss1429723995 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1580363364 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1609151490 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1652145523 Apr 01, 2015 (144)
38 EVA_MGP ss1711045425 Apr 01, 2015 (144)
39 HAMMER_LAB ss1800716754 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1922849496 Feb 12, 2016 (147)
41 JJLAB ss2022001342 Sep 14, 2016 (149)
42 USC_VALOUEV ss2150102656 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2259500555 Dec 20, 2016 (150)
44 TOPMED ss2426894053 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2625501817 Nov 08, 2017 (151)
46 ILLUMINA ss2634065549 Nov 08, 2017 (151)
47 GRF ss2705530443 Nov 08, 2017 (151)
48 GNOMAD ss2804148970 Nov 08, 2017 (151)
49 SWEGEN ss2993902577 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3024770827 Nov 08, 2017 (151)
51 CSHL ss3345471197 Nov 08, 2017 (151)
52 TOPMED ss3417032791 Nov 08, 2017 (151)
53 TOPMED ss3417032792 Nov 08, 2017 (151)
54 ILLUMINA ss3628874107 Oct 12, 2018 (152)
55 ILLUMINA ss3632005807 Oct 12, 2018 (152)
56 OMUKHERJEE_ADBS ss3646297287 Oct 12, 2018 (152)
57 URBANLAB ss3647622054 Oct 12, 2018 (152)
58 EGCUT_WGS ss3661864458 Jul 13, 2019 (153)
59 EVA_DECODE ss3711146679 Jul 13, 2019 (153)
60 ACPOP ss3730736019 Jul 13, 2019 (153)
61 EVA ss3761231034 Jul 13, 2019 (153)
62 KHV_HUMAN_GENOMES ss3804370809 Jul 13, 2019 (153)
63 EVA ss3825649545 Apr 25, 2020 (154)
64 EVA ss3828303681 Apr 25, 2020 (154)
65 EVA ss3837583488 Apr 25, 2020 (154)
66 EVA ss3843016492 Apr 25, 2020 (154)
67 SGDP_PRJ ss3857904723 Apr 25, 2020 (154)
68 KRGDB ss3904003164 Apr 25, 2020 (154)
69 FSA-LAB ss3984271557 Apr 26, 2021 (155)
70 FSA-LAB ss3984271558 Apr 26, 2021 (155)
71 EVA ss3986025977 Apr 26, 2021 (155)
72 EVA ss3986266167 Apr 26, 2021 (155)
73 TOPMED ss4598844926 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5163571135 Apr 26, 2021 (155)
75 1000Genomes NC_000003.11 - 194124624 Oct 12, 2018 (152)
76 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 194124624 Oct 12, 2018 (152)
77 Genetic variation in the Estonian population NC_000003.11 - 194124624 Oct 12, 2018 (152)
78 The Danish reference pan genome NC_000003.11 - 194124624 Apr 25, 2020 (154)
79 gnomAD - Genomes NC_000003.12 - 194403895 Apr 26, 2021 (155)
80 Genome of the Netherlands Release 5 NC_000003.11 - 194124624 Apr 25, 2020 (154)
81 KOREAN population from KRGDB NC_000003.11 - 194124624 Apr 25, 2020 (154)
82 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 194124624 Apr 25, 2020 (154)
83 Northern Sweden NC_000003.11 - 194124624 Jul 13, 2019 (153)
84 Qatari NC_000003.11 - 194124624 Apr 25, 2020 (154)
85 SGDP_PRJ NC_000003.11 - 194124624 Apr 25, 2020 (154)
86 Siberian NC_000003.11 - 194124624 Apr 25, 2020 (154)
87 8.3KJPN NC_000003.11 - 194124624 Apr 26, 2021 (155)
88 TopMed NC_000003.12 - 194403895 Apr 26, 2021 (155)
89 UK 10K study - Twins NC_000003.11 - 194124624 Oct 12, 2018 (152)
90 ALFA NC_000003.12 - 194403895 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)
rs3181401 Jul 03, 2002 (106)
rs3772199 Oct 08, 2002 (108)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
6171915771, ss3417032791 NC_000003.12:194403894:C:A NC_000003.12:194403894:C:A (self)
ss78855897 NC_000003.9:195605920:C:T NC_000003.12:194403894:C:T (self)
ss111600795, ss117441690, ss162951791, ss165378272, ss203687679, ss206135599, ss277519337, ss284821452, ss293011366, ss484544834 NC_000003.10:195605912:C:T NC_000003.12:194403894:C:T (self)
19244984, 10734266, 7602706, 6528303, 4716566, 11180558, 161185, 4020884, 4891426, 9921703, 2619010, 21540442, 10734266, ss220671419, ss232208483, ss239541278, ss484316589, ss536500275, ss650972649, ss779531607, ss782604493, ss835002174, ss979626638, ss1071185431, ss1307913714, ss1429723995, ss1580363364, ss1609151490, ss1652145523, ss1711045425, ss1800716754, ss1922849496, ss2022001342, ss2150102656, ss2426894053, ss2625501817, ss2634065549, ss2705530443, ss2804148970, ss2993902577, ss3345471197, ss3628874107, ss3632005807, ss3646297287, ss3661864458, ss3730736019, ss3761231034, ss3825649545, ss3828303681, ss3837583488, ss3857904723, ss3904003164, ss3984271557, ss3984271558, ss3986025977, ss3986266167, ss5163571135 NC_000003.11:194124623:C:T NC_000003.12:194403894:C:T (self)
136621264, 272693932, 436222481, 6171915771, ss2259500555, ss3024770827, ss3417032792, ss3647622054, ss3711146679, ss3804370809, ss3843016492, ss4598844926 NC_000003.12:194403894:C:T NC_000003.12:194403894:C:T (self)
ss20185326, ss22027313 NT_005535.15:68115:C:T NC_000003.12:194403894:C:T (self)
ss16795, ss1508758, ss4403185, ss4958260, ss44382960, ss96088636, ss133183715, ss156689392 NT_029928.13:77372:C:T NC_000003.12:194403894: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 rs14414

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