Name: rs36022183
Published: September 21, 2022
License: Open Access

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.

rs36022183

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:18653454 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.003328 (881/264690, TOPMED)
T=0.004214 (769/182476, GnomAD_exome)
T=0.003450 (358/103766, GnomAD) (+ 11 more)
T=0.00408 (328/80375, ExAC)
T=0.00630 (190/30180, ALFA)
T=0.00293 (31/10563, GO-ESP)
T=0.0017 (8/4805, 1000G_30x)
T=0.0013 (5/3775, 1000G)
T=0.0046 (17/3708, TWINSUK)
T=0.0031 (9/2889, ALSPAC)
T=0.007 (4/534, MGP)
T=0.004 (2/462, HapMap)
T=0.019 (2/108, Qatari)
T=0.05 (2/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CDKL5 : Missense Variant
RS1 : Intron Variant
Publications: 7 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	30180	C=0.99370	T=0.00630
European	Sub	22374	C=0.99312	T=0.00688
African	Sub	3688	C=0.9992	T=0.0008
African Others	Sub	124	C=1.000	T=0.000
African American	Sub	3564	C=0.9992	T=0.0008
Asian	Sub	172	C=1.000	T=0.000
East Asian	Sub	114	C=1.000	T=0.000
Other Asian	Sub	58	C=1.00	T=0.00
Latin American 1	Sub	154	C=0.968	T=0.032
Latin American 2	Sub	616	C=0.998	T=0.002
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	3078	C=0.9912	T=0.0088

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.996672	T=0.003328
gnomAD - Exomes	Global	Study-wide	182476	C=0.995786	T=0.004214
gnomAD - Exomes	European	Sub	97224	C=0.99527	T=0.00473
gnomAD - Exomes	Asian	Sub	32789	C=0.99930	T=0.00070
gnomAD - Exomes	American	Sub	27379	C=0.99799	T=0.00201
gnomAD - Exomes	African	Sub	13097	C=0.99916	T=0.00084
gnomAD - Exomes	Ashkenazi Jewish	Sub	7469	C=0.9742	T=0.0258
gnomAD - Exomes	Other	Sub	4518	C=0.9940	T=0.0060
gnomAD - Genomes	Global	Study-wide	103766	C=0.996550	T=0.003450
gnomAD - Genomes	European	Sub	57028	C=0.99576	T=0.00424
gnomAD - Genomes	African	Sub	31158	C=0.99933	T=0.00067
gnomAD - Genomes	American	Sub	9268	C=0.9986	T=0.0014
gnomAD - Genomes	Ashkenazi Jewish	Sub	2523	C=0.9707	T=0.0293
gnomAD - Genomes	East Asian	Sub	2241	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	1548	C=0.9948	T=0.0052
ExAC	Global	Study-wide	80375	C=0.99592	T=0.00408
ExAC	Europe	Sub	47867	C=0.99377	T=0.00623
ExAC	Asian	Sub	15146	C=0.99947	T=0.00053
ExAC	American	Sub	8832	C=0.9984	T=0.0016
ExAC	African	Sub	7967	C=0.9995	T=0.0005
ExAC	Other	Sub	563	C=0.993	T=0.007
Allele Frequency Aggregator	Total	Global	30180	C=0.99370	T=0.00630
Allele Frequency Aggregator	European	Sub	22374	C=0.99312	T=0.00688
Allele Frequency Aggregator	African	Sub	3688	C=0.9992	T=0.0008
Allele Frequency Aggregator	Other	Sub	3078	C=0.9912	T=0.0088
Allele Frequency Aggregator	Latin American 2	Sub	616	C=0.998	T=0.002
Allele Frequency Aggregator	Asian	Sub	172	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	154	C=0.968	T=0.032
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
GO Exome Sequencing Project	Global	Study-wide	10563	C=0.99707	T=0.00293
GO Exome Sequencing Project	European American	Sub	6728	C=0.9954	T=0.0046
GO Exome Sequencing Project	African American	Sub	3835	C=1.0000	T=0.0000
1000Genomes_30x	Global	Study-wide	4805	C=0.9983	T=0.0017
1000Genomes_30x	African	Sub	1328	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	961	C=0.992	T=0.008
1000Genomes_30x	South Asian	Sub	883	C=1.000	T=0.000
1000Genomes_30x	East Asian	Sub	878	C=1.000	T=0.000
1000Genomes_30x	American	Sub	755	C=1.000	T=0.000
1000Genomes	Global	Study-wide	3775	C=0.9987	T=0.0013
1000Genomes	African	Sub	1003	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	766	C=0.993	T=0.007
1000Genomes	East Asian	Sub	764	C=1.000	T=0.000
1000Genomes	South Asian	Sub	718	C=1.000	T=0.000
1000Genomes	American	Sub	524	C=1.000	T=0.000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9954	T=0.0046
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	C=0.9969	T=0.0031
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.993	T=0.007
HapMap	Global	Study-wide	462	C=0.996	T=0.004
HapMap	African	Sub	286	C=0.997	T=0.003
HapMap	Europe	Sub	176	C=0.994	T=0.006
Qatari	Global	Study-wide	108	C=0.981	T=0.019
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05

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.18653454C>G
GRCh38.p14 chr X	NC_000023.11:g.18653454C>T
GRCh37.p13 chr X	NC_000023.10:g.18671574C>G
GRCh37.p13 chr X	NC_000023.10:g.18671574C>T
RS1 RefSeqGene (LRG_702)	NG_008659.3:g.28995G>C
RS1 RefSeqGene (LRG_702)	NG_008659.3:g.28995G>A
CDKL5 RefSeqGene	NG_008475.1:g.232850C>G
CDKL5 RefSeqGene	NG_008475.1:g.232850C>T

Gene: RS1, retinoschisin 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RS1 transcript	NM_000330.4:c.184+3199G>C	N/A	Intron Variant
RS1 transcript variant X1	XM_047442337.1:c.	N/A	Genic Upstream Transcript Variant

Gene: CDKL5, cyclin dependent kinase like 5 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CDKL5 transcript variant III	NM_001323289.2:c.	N/A	Genic Downstream Transcript Variant
CDKL5 transcript variant II	NM_001037343.2:c.3003C>G	H [CAC] > Q [CAG]	Coding Sequence Variant
cyclin-dependent kinase-like 5 isoform 1	NP_001032420.1:p.His1001G… NP_001032420.1:p.His1001Gln	H (His) > Q (Gln)	Missense Variant
CDKL5 transcript variant II	NM_001037343.2:c.3003C>T	H [CAC] > H [CAT]	Coding Sequence Variant
cyclin-dependent kinase-like 5 isoform 1	NP_001032420.1:p.His1001=	H (His) > H (His)	Synonymous Variant
CDKL5 transcript variant I	NM_003159.3:c.3003C>G	H [CAC] > Q [CAG]	Coding Sequence Variant
cyclin-dependent kinase-like 5 isoform 1	NP_003150.1:p.His1001Gln	H (His) > Q (Gln)	Missense Variant
CDKL5 transcript variant I	NM_003159.3:c.3003C>T	H [CAC] > H [CAT]	Coding Sequence Variant
cyclin-dependent kinase-like 5 isoform 1	NP_003150.1:p.His1001=	H (His) > H (His)	Synonymous Variant

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: G (allele ID: 153546 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000133362.3	not provided	Not-Provided

Allele: T (allele ID: 100011 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000080072.17	not specified	Benign
RCV000233485.13	not provided	Uncertain-Significance
RCV000600588.2	Developmental and epileptic encephalopathy, 2	Likely-Benign
RCV000717700.2	History of neurodevelopmental disorder	Likely-Benign
RCV001084065.6	Angelman syndrome-like,Developmental and epileptic encephalopathy, 2	Benign

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=	G	T
GRCh38.p14 chr X	NC_000023.11:g.18653454=	NC_000023.11:g.18653454C>G	NC_000023.11:g.18653454C>T
GRCh37.p13 chr X	NC_000023.10:g.18671574=	NC_000023.10:g.18671574C>G	NC_000023.10:g.18671574C>T
RS1 RefSeqGene (LRG_702)	NG_008659.3:g.28995=	NG_008659.3:g.28995G>C	NG_008659.3:g.28995G>A
CDKL5 RefSeqGene	NG_008475.1:g.232850=	NG_008475.1:g.232850C>G	NG_008475.1:g.232850C>T
CDKL5 transcript variant I	NM_003159.3:c.3003=	NM_003159.3:c.3003C>G	NM_003159.3:c.3003C>T
CDKL5 transcript variant I	NM_003159.2:c.3003=	NM_003159.2:c.3003C>G	NM_003159.2:c.3003C>T
CDKL5 transcript variant II	NM_001037343.2:c.3003=	NM_001037343.2:c.3003C>G	NM_001037343.2:c.3003C>T
CDKL5 transcript variant II	NM_001037343.1:c.3003=	NM_001037343.1:c.3003C>G	NM_001037343.1:c.3003C>T
cyclin-dependent kinase-like 5 isoform 1	NP_003150.1:p.His1001=	NP_003150.1:p.His1001Gln	NP_003150.1:p.His1001=
cyclin-dependent kinase-like 5 isoform 1	NP_001032420.1:p.His1001=	NP_001032420.1:p.His1001Gln	NP_001032420.1:p.His1001=
RS1 transcript	NM_000330.3:c.184+3199=	NM_000330.3:c.184+3199G>C	NM_000330.3:c.184+3199G>A
RS1 transcript	NM_000330.4:c.184+3199=	NM_000330.4:c.184+3199G>C	NM_000330.4:c.184+3199G>A

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#.

38 SubSNP, 14 Frequency, 6 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	APPLERA_GI	ss48410524	Mar 15, 2006 (126)
2	CANCER-GENOME	ss74802778	Dec 07, 2007 (129)
3	ILLUMINA	ss74989005	Dec 07, 2007 (129)
4	KRIBB_YJKIM	ss119920259	Dec 01, 2009 (131)
5	ILLUMINA	ss173607842	Jul 04, 2010 (132)
6	1000GENOMES	ss341341058	May 09, 2011 (134)
7	NHLBI-ESP	ss342550490	May 09, 2011 (134)
8	1000GENOMES	ss491198543	May 04, 2012 (137)
9	CLINSEQ_SNP	ss491949131	May 04, 2012 (137)
10	ILLUMINA	ss537182249	Sep 08, 2015 (146)
11	CHWRETT	ss538296221	Aug 08, 2012 (137)
12	CHWRETT	ss538296298	Aug 08, 2012 (137)
13	CHWRETT	ss538296860	Aug 08, 2012 (137)
14	JMKIDD_LAB	ss1067609194	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1082815303	Aug 21, 2014 (142)
16	1000GENOMES	ss1553687882	Apr 01, 2015 (144)
17	EVA_GENOME_DK	ss1583339831	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1640416413	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1683410446	Apr 01, 2015 (144)
20	EVA_EXAC	ss1694468995	Apr 01, 2015 (144)
21	EVA_MGP	ss1711578206	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1939182819	Feb 12, 2016 (147)
23	HUMAN_LONGEVITY	ss2316006415	Dec 20, 2016 (150)
24	GNOMAD	ss2745324098	Nov 08, 2017 (151)
25	GNOMAD	ss2746082423	Nov 08, 2017 (151)
26	GNOMAD	ss2976937299	Nov 08, 2017 (151)
27	SWEGEN	ss3019695261	Nov 08, 2017 (151)
28	ILLUMINA	ss3630403727	Oct 12, 2018 (152)
29	ILLUMINA	ss3638848712	Oct 12, 2018 (152)
30	ILLUMINA	ss3643773301	Oct 12, 2018 (152)
31	EVA	ss3825475140	Apr 27, 2020 (154)
32	EVA	ss3986874151	Apr 26, 2021 (155)
33	TOPMED	ss5116884395	Apr 26, 2021 (155)
34	EVA	ss5237677059	Oct 16, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5311943101	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5503675547	Oct 16, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5619846895	Oct 16, 2022 (156)
38	EVA	ss5977907040	Oct 16, 2022 (156)
39	1000Genomes	NC_000023.10 - 18671574	Oct 12, 2018 (152)
40	1000Genomes_30x	NC_000023.11 - 18653454	Oct 16, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 18671574	Oct 12, 2018 (152)
42	ExAC	NC_000023.10 - 18671574	Oct 12, 2018 (152)
43	The Danish reference pan genome	NC_000023.10 - 18671574	Apr 27, 2020 (154)
44	gnomAD - Genomes	NC_000023.11 - 18653454	Apr 26, 2021 (155)
45	gnomAD - Exomes	NC_000023.10 - 18671574	Jul 13, 2019 (153)
46	GO Exome Sequencing Project	NC_000023.10 - 18671574	Oct 12, 2018 (152)
47	HapMap	NC_000023.11 - 18653454	Apr 27, 2020 (154)
48	Medical Genome Project healthy controls from Spanish population	NC_000023.10 - 18671574	Apr 27, 2020 (154)
49	Qatari	NC_000023.10 - 18671574	Apr 27, 2020 (154)
50	TopMed	NC_000023.11 - 18653454	Apr 26, 2021 (155)
51	UK 10K study - Twins	NC_000023.10 - 18671574	Oct 12, 2018 (152)
52	ALFA	NC_000023.11 - 18653454	Apr 26, 2021 (155)
53	ClinVar	RCV000080072.17	Oct 16, 2022 (156)
54	ClinVar	RCV000133362.3	Oct 16, 2022 (156)
55	ClinVar	RCV000233485.13	Oct 16, 2022 (156)
56	ClinVar	RCV000600588.2	Oct 16, 2022 (156)
57	ClinVar	RCV000717700.2	Oct 16, 2022 (156)
58	ClinVar	RCV001084065.6	Oct 16, 2022 (156)

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
RCV000133362.3, ss538296221	NC_000023.11:18653453:C:G	NC_000023.11:18653453:C:G	(self)
ss491949131, ss3643773301	NC_000023.9:18581494:C:T	NC_000023.11:18653453:C:T	(self)
81670166, 45114341, 9966951, 9504768, 14660347, 1931944, 693966, 21224741, 45114341, ss341341058, ss342550490, ss491198543, ss537182249, ss1067609194, ss1082815303, ss1553687882, ss1583339831, ss1640416413, ss1683410446, ss1694468995, ss1711578206, ss1939182819, ss2745324098, ss2746082423, ss2976937299, ss3019695261, ss3630403727, ss3638848712, ss3825475140, ss3986874151, ss5977907040	NC_000023.10:18671573:C:T	NC_000023.11:18653453:C:T	(self)
RCV000080072.17, RCV000233485.13, RCV000600588.2, RCV000717700.2, RCV001084065.6, 107372830, 576246160, 3954342, 680490752, 8554620615, ss538296298, ss538296860, ss2316006415, ss5116884395, ss5237677059, ss5311943101, ss5503675547, ss5619846895	NC_000023.11:18653453:C:T	NC_000023.11:18653453:C:T	(self)
ss48410524, ss74802778, ss74989005, ss119920259, ss173607842	NT_167197.1:16553335:C:T	NC_000023.11:18653453:C:T	(self)

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

7 citations for rs36022183

PMID	Title	Author	Year	Journal
15499549	Mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5/STK9) gene are associated with severe neurodevelopmental retardation.	Tao J et al.	2004	American journal of human genetics
18414213	ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.	Richards CS et al.	2008	Genetics in medicine
19241098	Novel mutations in the CDKL5 gene, predicted effects and associated phenotypes.	Russo S et al.	2009	Neurogenetics
20479760	Systematic resequencing of X-chromosome synaptic genes in autism spectrum disorder and schizophrenia.	Piton A et al.	2011	Molecular psychiatry
21160487	Analysis of Hungarian patients with Rett syndrome phenotype for MECP2, CDKL5 and FOXG1 gene mutations.	Hadzsiev K et al.	2011	Journal of human genetics
22867051	CDKL5 gene status in female patients with epilepsy and Rett-like features: two new mutations in the catalytic domain.	Maortua H et al.	2012	BMC medical genetics
23757202	Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.	Bean LJ et al.	2013	Human mutation

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs36022183