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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.

rs3752484

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:18620084 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.491458 (130084/264690, TOPMED)
A=0.444128 (45949/103459, GnomAD)
T=0.31818 (7071/22223, 14KJPN) (+ 15 more)
A=0.37133 (6877/18520, ALFA)
T=0.31753 (4078/12843, 8.3KJPN)
T=0.4229 (2032/4805, 1000G_30x)
T=0.4289 (1619/3775, 1000G)
A=0.3128 (1160/3708, TWINSUK)
T=0.2942 (862/2930, KOREAN)
A=0.3212 (928/2889, ALSPAC)
T=0.3967 (745/1878, HapMap)
T=0.109 (38/350, SGDP_PRJ)
T=0.500 (54/108, Qatari)
A=0.500 (54/108, Qatari)
T=0.38 (18/48, Vietnamese)
A=0.35 (14/40, GENOME_DK)
T=0.22 (4/18, Siberian)
A=0.0 (0/4, Ancient Sardinia)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CDKL5 : Intron Variant
Publications
2 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 18520 T=0.62867 A=0.37133
European Sub 14152 T=0.71099 A=0.28901
African Sub 2898 T=0.3620 A=0.6380
African Others Sub 114 T=0.430 A=0.570
African American Sub 2784 T=0.3592 A=0.6408
Asian Sub 112 T=0.268 A=0.732
East Asian Sub 86 T=0.27 A=0.73
Other Asian Sub 26 T=0.27 A=0.73
Latin American 1 Sub 146 T=0.370 A=0.630
Latin American 2 Sub 610 T=0.293 A=0.707
South Asian Sub 98 T=0.40 A=0.60
Other Sub 504 T=0.456 A=0.544


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 T=0.508542 A=0.491458
gnomAD - Genomes Global Study-wide 103459 T=0.555872 A=0.444128
gnomAD - Genomes European Sub 56915 T=0.69542 A=0.30458
gnomAD - Genomes African Sub 31072 T=0.37629 A=0.62371
gnomAD - Genomes American Sub 9222 T=0.3713 A=0.6287
gnomAD - Genomes Ashkenazi Jewish Sub 2507 T=0.5377 A=0.4623
gnomAD - Genomes East Asian Sub 2186 T=0.3152 A=0.6848
gnomAD - Genomes Other Sub 1557 T=0.4990 A=0.5010
14KJPN JAPANESE Study-wide 22223 T=0.31818 A=0.68182
Allele Frequency Aggregator Total Global 18520 T=0.62867 A=0.37133
Allele Frequency Aggregator European Sub 14152 T=0.71099 A=0.28901
Allele Frequency Aggregator African Sub 2898 T=0.3620 A=0.6380
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.293 A=0.707
Allele Frequency Aggregator Other Sub 504 T=0.456 A=0.544
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.370 A=0.630
Allele Frequency Aggregator Asian Sub 112 T=0.268 A=0.732
Allele Frequency Aggregator South Asian Sub 98 T=0.40 A=0.60
8.3KJPN JAPANESE Study-wide 12843 T=0.31753 A=0.68247
1000Genomes_30x Global Study-wide 4805 T=0.4229 A=0.5771
1000Genomes_30x African Sub 1328 T=0.3163 A=0.6837
1000Genomes_30x Europe Sub 961 T=0.681 A=0.319
1000Genomes_30x South Asian Sub 883 T=0.471 A=0.529
1000Genomes_30x East Asian Sub 878 T=0.319 A=0.681
1000Genomes_30x American Sub 755 T=0.347 A=0.653
1000Genomes Global Study-wide 3775 T=0.4289 A=0.5711
1000Genomes African Sub 1003 T=0.3240 A=0.6760
1000Genomes Europe Sub 766 T=0.679 A=0.321
1000Genomes East Asian Sub 764 T=0.317 A=0.683
1000Genomes South Asian Sub 718 T=0.486 A=0.514
1000Genomes American Sub 524 T=0.349 A=0.651
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6872 A=0.3128
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.2942 A=0.7058, C=0.0000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 T=0.6788 A=0.3212
HapMap Global Study-wide 1878 T=0.3967 A=0.6033
HapMap American Sub 768 T=0.464 A=0.536
HapMap African Sub 684 T=0.292 A=0.708
HapMap Asian Sub 254 T=0.311 A=0.689
HapMap Europe Sub 172 T=0.640 A=0.360
SGDP_PRJ Global Study-wide 350 T=0.109 A=0.891
Qatari Global Study-wide 108 T=0.500 A=0.500
A Vietnamese Genetic Variation Database Global Study-wide 48 T=0.38 A=0.62
The Danish reference pan genome Danish Study-wide 40 T=0.65 A=0.35
Siberian Global Study-wide 18 T=0.22 A=0.78
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 4 T=1.0 A=0.0
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.18620084T>A
GRCh38.p14 chr X NC_000023.11:g.18620084T>C
GRCh37.p13 chr X NC_000023.10:g.18638204T>A
GRCh37.p13 chr X NC_000023.10:g.18638204T>C
CDKL5 RefSeqGene NG_008475.1:g.199480T>A
CDKL5 RefSeqGene NG_008475.1:g.199480T>C
Gene: CDKL5, cyclin dependent kinase like 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDKL5 transcript variant II NM_001037343.2:c.2376+118…

NM_001037343.2:c.2376+118T>A

N/A Intron Variant
CDKL5 transcript variant III NM_001323289.2:c.2376+118…

NM_001323289.2:c.2376+118T>A

N/A Intron Variant
CDKL5 transcript variant I NM_003159.3:c.2376+118T>A 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.

Allele: A (allele ID: 165875 )
ClinVar Accession Disease Names Clinical Significance
RCV000144126.2 not provided Benign
RCV000169958.2 not specified Benign
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 T= A C
GRCh38.p14 chr X NC_000023.11:g.18620084= NC_000023.11:g.18620084T>A NC_000023.11:g.18620084T>C
GRCh37.p13 chr X NC_000023.10:g.18638204= NC_000023.10:g.18638204T>A NC_000023.10:g.18638204T>C
CDKL5 RefSeqGene NG_008475.1:g.199480= NG_008475.1:g.199480T>A NG_008475.1:g.199480T>C
CDKL5 transcript variant II NM_001037343.1:c.2376+118= NM_001037343.1:c.2376+118T>A NM_001037343.1:c.2376+118T>C
CDKL5 transcript variant II NM_001037343.2:c.2376+118= NM_001037343.2:c.2376+118T>A NM_001037343.2:c.2376+118T>C
CDKL5 transcript variant III NM_001323289.2:c.2376+118= NM_001323289.2:c.2376+118T>A NM_001323289.2:c.2376+118T>C
CDKL5 transcript variant I NM_003159.2:c.2376+118= NM_003159.2:c.2376+118T>A NM_003159.2:c.2376+118T>C
CDKL5 transcript variant I NM_003159.3:c.2376+118= NM_003159.3:c.2376+118T>A NM_003159.3:c.2376+118T>C
CDKL5 transcript variant X1 XM_005274584.1:c.2376+118= XM_005274584.1:c.2376+118T>A XM_005274584.1:c.2376+118T>C
CDKL5 transcript variant X2 XM_005274585.1:c.2325+118= XM_005274585.1:c.2325+118T>A XM_005274585.1:c.2325+118T>C
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#.

62 SubSNP, 17 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4938512 Aug 28, 2002 (107)
2 SC_SNP ss8181488 Apr 21, 2003 (114)
3 SC_SNP ss8528159 Jul 11, 2003 (116)
4 CSHL-HAPMAP ss18035986 Feb 27, 2004 (120)
5 PERLEGEN ss23823888 Sep 20, 2004 (123)
6 ABI ss43539822 Mar 13, 2006 (126)
7 SI_EXO ss61706081 Oct 14, 2006 (127)
8 ILLUMINA ss65792266 Oct 14, 2006 (127)
9 AFFY ss76820908 Dec 07, 2007 (129)
10 HGSV ss83522817 Dec 15, 2007 (130)
11 HGSV ss85497982 Dec 15, 2007 (130)
12 HGSV ss85638320 Dec 15, 2007 (130)
13 KRIBB_YJKIM ss104887421 Feb 05, 2009 (130)
14 BGI ss105717300 Feb 05, 2009 (130)
15 ILLUMINA-UK ss115596075 Feb 05, 2009 (130)
16 GMI ss157371133 Dec 01, 2009 (131)
17 ENSEMBL ss161780654 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss163048863 Jul 04, 2010 (132)
19 BUSHMAN ss204172495 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss208883658 Jul 04, 2010 (132)
21 GMI ss283705454 May 04, 2012 (137)
22 PJP ss294530827 May 09, 2011 (134)
23 1000GENOMES ss341340954 May 09, 2011 (134)
24 CHWRETT ss538296843 Aug 08, 2012 (137)
25 TISHKOFF ss566785254 Apr 25, 2013 (138)
26 SSMP ss662716956 Apr 25, 2013 (138)
27 JMKIDD_LAB ss1082815236 Aug 21, 2014 (142)
28 DDI ss1432011046 Apr 01, 2015 (144)
29 1000GENOMES ss1553687196 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1583339781 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1640416070 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1683410103 Apr 01, 2015 (144)
33 WEILL_CORNELL_DGM ss1939182691 Feb 12, 2016 (147)
34 GENOMED ss1971350029 Jul 19, 2016 (147)
35 USC_VALOUEV ss2158968666 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2316005007 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2629672795 Nov 08, 2017 (151)
38 GRF ss2710097113 Nov 08, 2017 (151)
39 GNOMAD ss2976935527 Nov 08, 2017 (151)
40 SWEGEN ss3019695015 Nov 08, 2017 (151)
41 BIOINF_KMB_FNS_UNIBA ss3029014369 Nov 08, 2017 (151)
42 OMUKHERJEE_ADBS ss3646571299 Oct 12, 2018 (152)
43 EVA ss3769964735 Jul 13, 2019 (153)
44 KHV_HUMAN_GENOMES ss3822810475 Jul 13, 2019 (153)
45 EVA ss3836106863 Apr 27, 2020 (154)
46 SGDP_PRJ ss3891081650 Apr 27, 2020 (154)
47 KRGDB ss3941430892 Apr 27, 2020 (154)
48 FSA-LAB ss3984439025 Apr 26, 2021 (155)
49 EVA ss3985931772 Apr 26, 2021 (155)
50 EVA ss3986874133 Apr 26, 2021 (155)
51 TOPMED ss5116878595 Apr 26, 2021 (155)
52 TOMMO_GENOMICS ss5233716631 Apr 26, 2021 (155)
53 1000G_HIGH_COVERAGE ss5311942558 Oct 16, 2022 (156)
54 HUGCELL_USP ss5503675039 Oct 16, 2022 (156)
55 1000G_HIGH_COVERAGE ss5619846094 Oct 16, 2022 (156)
56 SANFORD_IMAGENETICS ss5664941014 Oct 16, 2022 (156)
57 TOMMO_GENOMICS ss5795199703 Oct 16, 2022 (156)
58 YY_MCH ss5818917239 Oct 16, 2022 (156)
59 EVA ss5848739702 Oct 16, 2022 (156)
60 EVA ss5857026363 Oct 16, 2022 (156)
61 EVA ss5977906756 Oct 16, 2022 (156)
62 EVA ss5981323885 Oct 16, 2022 (156)
63 1000Genomes NC_000023.10 - 18638204 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000023.11 - 18620084 Oct 16, 2022 (156)
65 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 18638204 Oct 12, 2018 (152)
66 The Danish reference pan genome NC_000023.10 - 18638204 Apr 27, 2020 (154)
67 gnomAD - Genomes NC_000023.11 - 18620084 Apr 26, 2021 (155)
68 HapMap NC_000023.11 - 18620084 Apr 27, 2020 (154)
69 KOREAN population from KRGDB NC_000023.10 - 18638204 Apr 27, 2020 (154)
70 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000023.10 - 18638204 Apr 26, 2021 (155)
71 Qatari NC_000023.10 - 18638204 Apr 27, 2020 (154)
72 SGDP_PRJ NC_000023.10 - 18638204 Apr 27, 2020 (154)
73 Siberian NC_000023.10 - 18638204 Apr 27, 2020 (154)
74 8.3KJPN NC_000023.10 - 18638204 Apr 26, 2021 (155)
75 14KJPN NC_000023.11 - 18620084 Oct 16, 2022 (156)
76 TopMed NC_000023.11 - 18620084 Apr 26, 2021 (155)
77 UK 10K study - Twins NC_000023.10 - 18638204 Oct 12, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000023.10 - 18638204 Jul 13, 2019 (153)
79 ALFA NC_000023.11 - 18620084 Apr 26, 2021 (155)
80 ClinVar RCV000144126.2 Apr 27, 2020 (154)
81 ClinVar RCV000169958.2 Oct 16, 2022 (156)
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)
rs59929408 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83522817, ss85497982, ss85638320 NC_000023.8:18397860:T:A NC_000023.11:18620083:T:A (self)
ss76820908, ss115596075, ss163048863, ss204172495, ss208883658, ss283705454, ss294530827 NC_000023.9:18548124:T:A NC_000023.11:18620083:T:A (self)
81669486, 45113964, 9504718, 48608286, 1157699, 21224613, 43098630, 11485020, 91685938, 45113964, 9952220, ss341340954, ss566785254, ss662716956, ss1082815236, ss1432011046, ss1553687196, ss1583339781, ss1640416070, ss1683410103, ss1939182691, ss1971350029, ss2158968666, ss2629672795, ss2710097113, ss2976935527, ss3019695015, ss3646571299, ss3769964735, ss3836106863, ss3891081650, ss3941430892, ss3984439025, ss3985931772, ss3986874133, ss5233716631, ss5664941014, ss5848739702, ss5977906756, ss5981323885 NC_000023.10:18638203:T:A NC_000023.11:18620083:T:A (self)
RCV000144126.2, RCV000169958.2, 107372029, 576241877, 3954317, 129036807, 680484952, 7322246009, ss538296843, ss2316005007, ss3029014369, ss3822810475, ss5116878595, ss5311942558, ss5503675039, ss5619846094, ss5795199703, ss5818917239, ss5857026363 NC_000023.11:18620083:T:A NC_000023.11:18620083:T:A (self)
ss8528159 NT_011757.12:5552670:T:A NC_000023.11:18620083:T:A (self)
ss18035986 NT_011757.13:14604768:T:A NC_000023.11:18620083:T:A (self)
ss61706081 NT_011757.14:14604768:T:A NC_000023.11:18620083:T:A (self)
ss4938512, ss8181488, ss23823888, ss43539822, ss65792266, ss104887421, ss105717300, ss157371133, ss161780654 NT_167197.1:16519965:T:A NC_000023.11:18620083:T:A (self)
48608286, ss3941430892 NC_000023.10:18638203:T:C NC_000023.11:18620083:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs3752484
PMID Title Author Year Journal
16015284 Early onset seizures and Rett-like features associated with mutations in CDKL5. Evans JC et al. 2005 European journal of human genetics
20397747 Cyclin-dependent kinase-like 5 (CDKL5) mutation screening in Rett syndrome and related disorders. White R et al. 2010 Twin research and human genetics
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