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.
rs61752159
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chrX:18644530 (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>T
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
None
- Clinical Significance
- Reported in ClinVar
- Gene : Consequence
-
RS1 : Missense VariantCDKL5 : Intron Variant
- Publications
- 10 citations
- Genomic View
- See rs on genome
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").
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.
| Sequence name | Change |
|---|---|
| GRCh38.p14 chr X | NC_000023.11:g.18644530C>T |
| GRCh37.p13 chr X | NC_000023.10:g.18662650C>T |
| RS1 RefSeqGene (LRG_702) | NG_008659.3:g.37919G>A |
| CDKL5 RefSeqGene | NG_008475.1:g.223926C>T |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| CDKL5 transcript variant II |
NM_001037343.2:c.2714-147… NM_001037343.2:c.2714-1477C>T |
N/A | Intron Variant |
| CDKL5 transcript variant I | NM_003159.3:c.2714-1477C>T | N/A | Intron Variant |
| CDKL5 transcript variant III | NM_001323289.2:c. | N/A | Genic Downstream Transcript Variant |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| RS1 transcript | NM_000330.4:c.422G>A | R [CGC] > H [CAC] | Coding Sequence Variant |
| retinoschisin precursor | NP_000321.1:p.Arg141His | R (Arg) > H (His) | Missense Variant |
| RS1 transcript variant X1 | XM_047442337.1:c.326G>A | R [CGC] > H [CAC] | Coding Sequence Variant |
| retinoschisin isoform X1 | XP_047298293.1:p.Arg109His | R (Arg) > H (His) | Missense 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.
| ClinVar Accession | Disease Names | Clinical Significance |
|---|---|---|
| RCV000085301.5 | not provided | Pathogenic |
| RCV000411096.2 | Juvenile retinoschisis | Likely-Pathogenic |
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= | T |
|---|---|---|
| GRCh38.p14 chr X | NC_000023.11:g.18644530= | NC_000023.11:g.18644530C>T |
| GRCh37.p13 chr X | NC_000023.10:g.18662650= | NC_000023.10:g.18662650C>T |
| RS1 RefSeqGene (LRG_702) | NG_008659.3:g.37919= | NG_008659.3:g.37919G>A |
| RS1 transcript | NM_000330.4:c.422= | NM_000330.4:c.422G>A |
| RS1 transcript | NM_000330.3:c.422= | NM_000330.3:c.422G>A |
| CDKL5 RefSeqGene | NG_008475.1:g.223926= | NG_008475.1:g.223926C>T |
| RS1 transcript variant X1 | XM_047442337.1:c.326= | XM_047442337.1:c.326G>A |
| retinoschisin precursor | NP_000321.1:p.Arg141= | NP_000321.1:p.Arg141His |
| retinoschisin isoform X1 | XP_047298293.1:p.Arg109= | XP_047298293.1:p.Arg109His |
| CDKL5 transcript variant II | NM_001037343.1:c.2714-1477= | NM_001037343.1:c.2714-1477C>T |
| CDKL5 transcript variant II | NM_001037343.2:c.2714-1477= | NM_001037343.2:c.2714-1477C>T |
| CDKL5 transcript variant I | NM_003159.2:c.2714-1477= | NM_003159.2:c.2714-1477C>T |
| CDKL5 transcript variant I | NM_003159.3:c.2714-1477= | NM_003159.3:c.2714-1477C>T |
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#.
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | RISN-LSDB | ss562060587 | Dec 21, 2012 (137) |
| 2 | ClinVar | RCV000085301.5 | Oct 16, 2022 (156) |
| 3 | ClinVar | RCV000411096.2 | 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).
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 9618178 | Functional implications of the spectrum of mutations found in 234 cases with X-linked juvenile retinoschisis. The Retinoschisis Consortium. | 1998 | Human molecular genetics | |
| 10636429 | Clinical phenotype associated with the arg141 his mutation in the X-linked retinoschisis gene. | Park JH et al. | 2000 | Archives of ophthalmology (Chicago, Ill. |
| 16361673 | Molecular pathology of X linked retinoschisis: mutations interfere with retinoschisin secretion and oligomerisation. | Wang T et al. | 2006 | The British journal of ophthalmology |
| 17525175 | Coexpression and interaction of wild-type and missense RS1 mutants associated with X-linked retinoschisis: its relevance to gene therapy. | Dyka FM et al. | 2007 | Investigative ophthalmology & visual science |
| 17631851 | Unusual manifestations of x-linked retinoschisis: clinical profile and diagnostic evaluation. | Shukla D et al. | 2007 | American journal of ophthalmology |
| 18690710 | Characterization and purification of the discoidin domain-containing protein retinoschisin and its interaction with galactose. | Dyka FM et al. | 2008 | Biochemistry |
| 18834580 | Relation of response to treatment with dorzolamide in X-linked retinoschisis to the mechanism of functional loss in retinoschisin. | Walia S et al. | 2009 | American journal of ophthalmology |
| 19093009 | Clinical and genetic findings in Hungarian patients with X-linked juvenile retinoschisis. | Lesch B et al. | 2008 | Molecular vision |
| 20061330 | Molecular modeling of retinoschisin with functional analysis of pathogenic mutations from human X-linked retinoschisis. | Sergeev YV et al. | 2010 | Human molecular genetics |
| 30652005 | Novel mutations in the RS1 gene in Japanese patients with X-linked congenital retinoschisis. | Kondo H et al. | 2019 | Human genome variation |
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.