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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs35086888

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr17:3647506 (GRCh38.p7) 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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00429 (1057/246180, GnomAD)
A=0.01939 (2435/125568, TOPMED)
A=0.00545 (660/121160, ExAC) (+ 4 more)
A=0.0183 (567/30960, GnomAD)
A=0.018 (88/5008, 1000G)
A=0.000 (1/3854, ALSPAC)
A=0.000 (0/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CTNS : Missense Variant
LOC105371493 : Intron Variant
Publications
2 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.p7 chr 17 NC_000017.11:g.3647506G>A
GRCh37.p13 chr 17 NC_000017.10:g.3550800G>A
CTNS RefSeqGene NG_012489.1:g.16039G>A
Gene: CTNS, cystinosin, lysosomal cystine transporter (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CTNS transcript variant 2 NM_004937.2:c.124G>A V [GTC] > I [ATC] Coding Sequence Variant
cystinosin isoform 2 precursor NP_004928.2:p.Val...

NP_004928.2:p.Val42Ile

V (Val) > I (Ile) Missense Variant
CTNS transcript variant 1 NM_001031681.2:c....

NM_001031681.2:c.124G>A

V [GTC] > I [ATC] Coding Sequence Variant
cystinosin isoform 1 precursor NP_001026851.2:p....

NP_001026851.2:p.Val42Ile

V (Val) > I (Ile) Missense Variant
CTNS transcript variant X6 XM_017024254.1:c. N/A Intron Variant
CTNS transcript variant X9 XM_017024257.1:c. N/A Intron Variant
CTNS transcript variant X4 XM_006721464.2:c. N/A 5 Prime UTR Variant
CTNS transcript variant X5 XM_011523692.2:c. N/A 5 Prime UTR Variant
CTNS transcript variant X7 XM_017024255.1:c. N/A 5 Prime UTR Variant
CTNS transcript variant X8 XM_017024256.1:c. N/A 5 Prime UTR Variant
CTNS transcript variant X10 XM_017024258.1:c. N/A 5 Prime UTR Variant
CTNS transcript variant X1 XM_005256485.2:c....

XM_005256485.2:c.124G>A

V [GTC] > I [ATC] Coding Sequence Variant
cystinosin isoform X1 XP_005256542.1:p....

XP_005256542.1:p.Val42Ile

V (Val) > I (Ile) Missense Variant
CTNS transcript variant X2 XM_011523691.2:c....

XM_011523691.2:c.124G>A

V [GTC] > I [ATC] Coding Sequence Variant
cystinosin isoform X1 XP_011521993.1:p....

XP_011521993.1:p.Val42Ile

V (Val) > I (Ile) Missense Variant
CTNS transcript variant X3 XM_006721463.2:c....

XM_006721463.2:c.124G>A

V [GTC] > I [ATC] Coding Sequence Variant
cystinosin isoform X1 XP_006721526.1:p....

XP_006721526.1:p.Val42Ile

V (Val) > I (Ile) Missense Variant
Gene: LOC105371493, uncharacterized LOC105371493 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105371493 transcript variant X1 XR_001752758.1:n. N/A Intron Variant
LOC105371493 transcript variant X2 XR_001752759.1:n. N/A Intron Variant
LOC105371493 transcript variant X3 XR_001752760.1:n. N/A Intron Variant
LOC105371493 transcript variant X6 XR_001752761.1:n. N/A Intron Variant
LOC105371493 transcript variant X4 XR_934164.2:n. N/A Intron Variant
LOC105371493 transcript variant X6 XR_934165.2:n. 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.

Allele: A (allele ID: 19486 )
ClinVar Accession Disease Names Clinical Significance
RCV000004700.4 Cystinosis, atypical nephropathic Pathogenic
RCV000276289.1 Nephropathic cystinosis Likely-Benign
RCV000333816.1 Cystinosis Likely-Benign
RCV000440461.1 not provided Benign
RCV000630476.1 Cystinosis, ocular nonnephropathic,Juvenile nephropathic cystinosis,Nephropathic cystinosis Benign
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
The Genome Aggregation Database Global Study-wide 246180 G=0.99571 A=0.00429
The Genome Aggregation Database European Sub 133934 G=0.99990 A=0.00010
The Genome Aggregation Database Asian Sub 48030 G=0.9997 A=0.0003
The Genome Aggregation Database American Sub 33582 G=0.9976 A=0.0024
The Genome Aggregation Database African Sub 15298 G=0.9386 A=0.0614
The Genome Aggregation Database Ashkenazi Jewish Sub 9850 G=1.000 A=0.000
The Genome Aggregation Database Other Sub 5486 G=0.999 A=0.001
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.98061 A=0.01939
The Genome Aggregation Database Global Study-wide 30960 G=0.9817 A=0.0183
The Genome Aggregation Database European Sub 18498 G=1.0000 A=0.0000
The Genome Aggregation Database African Sub 8718 G=0.935 A=0.065
The Genome Aggregation Database East Asian Sub 1622 G=1.000 A=0.000
The Genome Aggregation Database Other Sub 982 G=1.00 A=0.00
The Genome Aggregation Database American Sub 838 G=1.00 A=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=1.00 A=0.00
1000Genomes Global Study-wide 5008 G=0.982 A=0.018
1000Genomes African Sub 1322 G=0.934 A=0.066
1000Genomes East Asian Sub 1008 G=1.000 A=0.000
1000Genomes Europe Sub 1006 G=1.000 A=0.000
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=1.000 A=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.000 A=0.000
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 G= A Note
GRCh38.p7 chr 17 NC_000017.11:g.3647506G= NC_000017.11:g.3647506G>A
GRCh37.p13 chr 17 NC_000017.10:g.3550800G= NC_000017.10:g.3550800G>A
CTNS RefSeqGene NG_012489.1:g.16039G= NG_012489.1:g.16039G>A
CTNS transcript variant 2 NM_004937.2:c.124G= NM_004937.2:c.124G>A
CTNS transcript variant 1 NM_001031681.2:c.124G= NM_001031681.2:c.124G>A
CTNS transcript variant X1 XM_005256485.2:c.124G= XM_005256485.2:c.124G>A
CTNS transcript variant X1 XM_005256485.1:c.124G= XM_005256485.1:c.124G>A
CTNS transcript variant X3 XM_006721463.2:c.124G= XM_006721463.2:c.124G>A
CTNS transcript variant X5 XM_011523692.2:c.-318G= XM_011523692.2:c.-318G>A
CTNS transcript variant X4 XM_006721464.2:c.-233G= XM_006721464.2:c.-233G>A
CTNS transcript variant X2 XM_011523691.2:c.124G= XM_011523691.2:c.124G>A
CTNS transcript variant X8 XM_017024256.1:c.-318G= XM_017024256.1:c.-318G>A
CTNS transcript variant X7 XM_017024255.1:c.-233G= XM_017024255.1:c.-233G>A
CTNS transcript variant X10 XM_017024258.1:c.-233G= XM_017024258.1:c.-233G>A
cystinosin isoform 2 precursor NP_004928.2:p.Val42= NP_004928.2:p.Val42Ile
cystinosin isoform 1 precursor NP_001026851.2:p.Val42= NP_001026851.2:p.Val42Ile
cystinosin isoform X1 XP_005256542.1:p.Val42= XP_005256542.1:p.Val42Ile
cystinosin isoform X1 XP_006721526.1:p.Val42= XP_006721526.1:p.Val42Ile
cystinosin isoform X1 XP_011521993.1:p.Val42= XP_011521993.1:p.Val42Ile
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#.

5 ClinVar, 7 Frequency, 45 SubSNP submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48427276 Mar 14, 2006 (126)
2 PERLEGEN ss69189535 May 17, 2007 (127)
3 ILLUMINA ss160625126 Dec 01, 2009 (131)
4 1000GENOMES ss227433653 Jul 14, 2010 (132)
5 OMICIA ss244239495 May 27, 2010 (132)
6 OMIM-CURATED-RECORDS ss262857572 Sep 17, 2010 (132)
7 NHLBI-ESP ss342439939 May 09, 2011 (134)
8 ILLUMINA ss480490158 May 04, 2012 (137)
9 ILLUMINA ss481715235 Sep 08, 2015 (146)
10 ILLUMINA ss483621834 May 04, 2012 (137)
11 1000GENOMES ss491112544 May 04, 2012 (137)
12 EXOME_CHIP ss491514817 May 04, 2012 (137)
13 ILLUMINA ss533773606 Sep 08, 2015 (146)
14 TISHKOFF ss565131910 Apr 25, 2013 (138)
15 ILLUMINA ss779453731 Sep 08, 2015 (146)
16 ILLUMINA ss780723219 Sep 08, 2015 (146)
17 ILLUMINA ss781244297 Sep 08, 2015 (146)
18 ILLUMINA ss783399103 Sep 08, 2015 (146)
19 ILLUMINA ss834923352 Sep 08, 2015 (146)
20 1000GENOMES ss1357687303 Aug 21, 2014 (142)
21 EVA_UK10K_ALSPAC ss1635175557 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1678169590 Apr 01, 2015 (144)
23 EVA_EXAC ss1692520816 Apr 01, 2015 (144)
24 ILLUMINA ss1752223092 Sep 08, 2015 (146)
25 ILLUMINA ss1917912734 Feb 12, 2016 (147)
26 WEILL_CORNELL_DGM ss1936310726 Feb 12, 2016 (147)
27 ILLUMINA ss1946425488 Feb 12, 2016 (147)
28 ILLUMINA ss1959715789 Feb 12, 2016 (147)
29 HUMAN_LONGEVITY ss2215067157 Dec 20, 2016 (150)
30 TOPMED ss2379906577 Dec 20, 2016 (150)
31 ILLUMINA ss2633367592 Nov 08, 2017 (151)
32 GNOMAD ss2742322136 Nov 08, 2017 (151)
33 GNOMAD ss2749652759 Nov 08, 2017 (151)
34 GNOMAD ss2947077743 Nov 08, 2017 (151)
35 AFFY ss2985082210 Nov 08, 2017 (151)
36 AFFY ss2985720898 Nov 08, 2017 (151)
37 ILLUMINA ss3021746729 Nov 08, 2017 (151)
38 TOPMED ss3255873878 Nov 08, 2017 (151)
39 ILLUMINA ss3627610588 Jul 20, 2018 (151)
40 ILLUMINA ss3627610589 Jul 20, 2018 (151)
41 ILLUMINA ss3631350561 Jul 20, 2018 (151)
42 ILLUMINA ss3634660572 Jul 20, 2018 (151)
43 ILLUMINA ss3636351745 Jul 20, 2018 (151)
44 ILLUMINA ss3640367891 Jul 20, 2018 (151)
45 ILLUMINA ss3644678562 Jul 20, 2018 (151)
46 1000Genomes NC_000017.10 - 3550800 Jul 20, 2018 (151)
47 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 3550800 Jul 20, 2018 (151)
48 The Exome Aggregation Consortium NC_000017.10 - 3550800 Jul 20, 2018 (151)
49 The Genome Aggregation Database NC_000017.10 - 3550800 Jul 20, 2018 (151)
50 The Genome Aggregation Database NC_000017.10 - 3550800 Jul 20, 2018 (151)
51 Trans-Omics for Precision Medicine NC_000017.11 - 3647506 Jul 20, 2018 (151)
52 UK 10K study - Twins NC_000017.10 - 3550800 Jul 20, 2018 (151)
53 ClinVar RCV000004700.4 Jul 20, 2018 (151)
54 ClinVar RCV000276289.1 Jul 20, 2018 (151)
55 ClinVar RCV000333816.1 Jul 20, 2018 (151)
56 ClinVar RCV000440461.1 Jul 20, 2018 (151)
57 ClinVar RCV000630476.1 Jul 20, 2018 (151)
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
ss483621834 NC_000017.9:3497548:G= NC_000017.11:3647505:G= (self)
70893086, 39318521, 2943874, 80779271, 11336871, 39318521, ss227433653, ss342439939, ss480490158, ss481715235, ss491112544, ss491514817, ss533773606, ss565131910, ss779453731, ss780723219, ss781244297, ss783399103, ss834923352, ss1357687303, ss1635175557, ss1678169590, ss1692520816, ss1752223092, ss1917912734, ss1936310726, ss1946425488, ss1959715789, ss2379906577, ss2633367592, ss2742322136, ss2749652759, ss2947077743, ss2985082210, ss2985720898, ss3021746729, ss3627610588, ss3627610589, ss3631350561, ss3634660572, ss3636351745, ss3640367891, ss3644678562 NC_000017.10:3550799:G= NC_000017.11:3647505:G= (self)
151740507, ss244239495, ss262857572, ss2215067157, ss3255873878 NC_000017.11:3647505:G= NC_000017.11:3647505:G= (self)
ss48427276, ss69189535, ss160625126 NT_010718.16:3154173:G= NC_000017.11:3647505:G= (self)
ss483621834 NC_000017.9:3497548:G>A NC_000017.11:3647505:G>A (self)
70893086, 39318521, 2943874, 80779271, 11336871, 39318521, ss227433653, ss342439939, ss480490158, ss481715235, ss491112544, ss491514817, ss533773606, ss565131910, ss779453731, ss780723219, ss781244297, ss783399103, ss834923352, ss1357687303, ss1635175557, ss1678169590, ss1692520816, ss1752223092, ss1917912734, ss1936310726, ss1946425488, ss1959715789, ss2379906577, ss2633367592, ss2742322136, ss2749652759, ss2947077743, ss2985082210, ss2985720898, ss3021746729, ss3627610588, ss3627610589, ss3631350561, ss3634660572, ss3636351745, ss3640367891, ss3644678562 NC_000017.10:3550799:G>A NC_000017.11:3647505:G>A (self)
RCV000004700.4, RCV000276289.1, RCV000333816.1, RCV000440461.1, RCV000630476.1, 151740507, ss244239495, ss262857572, ss2215067157, ss3255873878 NC_000017.11:3647505:G>A NC_000017.11:3647505:G>A (self)
ss48427276, ss69189535, ss160625126 NT_010718.16:3154173:G>A NC_000017.11:3647505:G>A (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 rs35086888
PMID Title Author Year Journal
10556299 Severity of phenotype in cystinosis varies with mutations in the CTNS gene: predicted effect on the model of cystinosin. Attard M et al. 1999 Human molecular genetics
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine

Genomic regions, transcripts, and products
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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: 0.1.4.post833+d3ba21e