Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

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.

rs137852818

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:41542717 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000 (0/478, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CASK : Missense Variant
Publications
1 citation
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 478 T=1.000 C=0.000
European Sub 0 T=0 C=0
African Sub 426 T=1.000 C=0.000
African Others Sub 0 T=0 C=0
African American Sub 426 T=1.000 C=0.000
Asian Sub 0 T=0 C=0
East Asian Sub 0 T=0 C=0
Other Asian Sub 0 T=0 C=0
Latin American 1 Sub 0 T=0 C=0
Latin American 2 Sub 0 T=0 C=0
South Asian Sub 0 T=0 C=0
Other Sub 52 T=1.00 C=0.00


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
Allele Frequency Aggregator Total Global 478 T=1.000 C=0.000
Allele Frequency Aggregator African Sub 426 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 52 T=1.00 C=0.00
Allele Frequency Aggregator European Sub 0 T=0 C=0
Allele Frequency Aggregator Latin American 1 Sub 0 T=0 C=0
Allele Frequency Aggregator Latin American 2 Sub 0 T=0 C=0
Allele Frequency Aggregator South Asian Sub 0 T=0 C=0
Allele Frequency Aggregator Asian Sub 0 T=0 C=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.41542717T>C
GRCh37.p13 chr X NC_000023.10:g.41401970T>C
CASK RefSeqGene NG_016754.2:g.385318A>G
Gene: CASK, calcium/calmodulin dependent serine protein kinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CASK transcript variant 1 NM_003688.3:c.2129A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform 1 NP_003679.2:p.Asp710Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant 2 NM_001126054.2:c.2060A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform 2 NP_001119526.1:p.Asp687Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant 3 NM_001126055.2:c.2042A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform 3 NP_001119527.1:p.Asp681Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant 4 NM_001367721.1:c.2129A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform 4 NP_001354650.1:p.Asp710Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X1 XM_011543993.3:c.2129A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X1 XP_011542295.1:p.Asp710Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X2 XM_005272686.5:c.2111A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X2 XP_005272743.1:p.Asp704Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X2 XM_011543994.3:c.2093A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X2 XP_011542296.1:p.Asp698Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X3 XM_047442601.1:c.2075A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X3 XP_047298557.1:p.Asp692Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X4 XM_011543995.3:c.2060A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X4 XP_011542297.1:p.Asp687Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X5 XM_011543996.3:c.2024A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X5 XP_011542298.1:p.Asp675Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X6 XM_006724566.4:c.2006A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X6 XP_006724629.1:p.Asp669Gly D (Asp) > G (Gly) Missense Variant
CASK transcript variant X7 XM_011543997.4:c.1556A>G D [GAT] > G [GGT] Coding Sequence Variant
peripheral plasma membrane protein CASK isoform X7 XP_011542299.1:p.Asp519Gly D (Asp) > G (Gly) Missense 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
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= C
GRCh38.p14 chr X NC_000023.11:g.41542717= NC_000023.11:g.41542717T>C
GRCh37.p13 chr X NC_000023.10:g.41401970= NC_000023.10:g.41401970T>C
CASK RefSeqGene NG_016754.2:g.385318= NG_016754.2:g.385318A>G
CASK transcript variant 1 NM_003688.4:c.2129= NM_003688.4:c.2129A>G
CASK transcript variant 1 NM_003688.3:c.2129= NM_003688.3:c.2129A>G
CASK transcript variant 2 NM_001126054.3:c.2060= NM_001126054.3:c.2060A>G
CASK transcript variant 2 NM_001126054.2:c.2060= NM_001126054.2:c.2060A>G
CASK transcript variant 3 NM_001126055.3:c.2042= NM_001126055.3:c.2042A>G
CASK transcript variant 3 NM_001126055.2:c.2042= NM_001126055.2:c.2042A>G
CASK transcript variant 4 NM_001367721.1:c.2129= NM_001367721.1:c.2129A>G
CASK transcript variant 5 NM_001410745.1:c.2111= NM_001410745.1:c.2111A>G
CASK transcript variant X2 XM_005272686.5:c.2111= XM_005272686.5:c.2111A>G
CASK transcript variant X6 XM_006724566.4:c.2006= XM_006724566.4:c.2006A>G
CASK transcript variant X6 XM_006724566.3:c.2006= XM_006724566.3:c.2006A>G
CASK transcript variant X6 XM_006724566.2:c.2006= XM_006724566.2:c.2006A>G
CASK transcript variant X4 XM_006724566.1:c.2006= XM_006724566.1:c.2006A>G
CASK transcript variant X7 XM_011543997.4:c.1556= XM_011543997.4:c.1556A>G
CASK transcript variant X7 XM_011543997.3:c.1556= XM_011543997.3:c.1556A>G
CASK transcript variant X7 XM_011543997.2:c.1556= XM_011543997.2:c.1556A>G
CASK transcript variant X7 XM_011543997.1:c.1556= XM_011543997.1:c.1556A>G
CASK transcript variant X1 XM_011543993.3:c.2129= XM_011543993.3:c.2129A>G
CASK transcript variant X1 XM_011543993.2:c.2129= XM_011543993.2:c.2129A>G
CASK transcript variant X1 XM_011543993.1:c.2129= XM_011543993.1:c.2129A>G
CASK transcript variant X2 XM_011543994.3:c.2093= XM_011543994.3:c.2093A>G
CASK transcript variant X3 XM_011543994.2:c.2093= XM_011543994.2:c.2093A>G
CASK transcript variant X3 XM_011543994.1:c.2093= XM_011543994.1:c.2093A>G
CASK transcript variant X4 XM_011543995.3:c.2060= XM_011543995.3:c.2060A>G
CASK transcript variant X4 XM_011543995.2:c.2060= XM_011543995.2:c.2060A>G
CASK transcript variant X4 XM_011543995.1:c.2060= XM_011543995.1:c.2060A>G
CASK transcript variant X5 XM_011543996.3:c.2024= XM_011543996.3:c.2024A>G
CASK transcript variant X5 XM_011543996.2:c.2024= XM_011543996.2:c.2024A>G
CASK transcript variant X5 XM_011543996.1:c.2024= XM_011543996.1:c.2024A>G
CASK transcript variant X3 XM_047442601.1:c.2075= XM_047442601.1:c.2075A>G
peripheral plasma membrane protein CASK isoform 1 NP_003679.2:p.Asp710= NP_003679.2:p.Asp710Gly
peripheral plasma membrane protein CASK isoform 2 NP_001119526.1:p.Asp687= NP_001119526.1:p.Asp687Gly
peripheral plasma membrane protein CASK isoform 3 NP_001119527.1:p.Asp681= NP_001119527.1:p.Asp681Gly
peripheral plasma membrane protein CASK isoform 4 NP_001354650.1:p.Asp710= NP_001354650.1:p.Asp710Gly
peripheral plasma membrane protein CASK isoform X2 XP_005272743.1:p.Asp704= XP_005272743.1:p.Asp704Gly
peripheral plasma membrane protein CASK isoform X6 XP_006724629.1:p.Asp669= XP_006724629.1:p.Asp669Gly
peripheral plasma membrane protein CASK isoform X7 XP_011542299.1:p.Asp519= XP_011542299.1:p.Asp519Gly
peripheral plasma membrane protein CASK isoform X1 XP_011542295.1:p.Asp710= XP_011542295.1:p.Asp710Gly
peripheral plasma membrane protein CASK isoform X2 XP_011542296.1:p.Asp698= XP_011542296.1:p.Asp698Gly
peripheral plasma membrane protein CASK isoform X4 XP_011542297.1:p.Asp687= XP_011542297.1:p.Asp687Gly
peripheral plasma membrane protein CASK isoform X5 XP_011542298.1:p.Asp675= XP_011542298.1:p.Asp675Gly
peripheral plasma membrane protein CASK isoform X3 XP_047298557.1:p.Asp692= XP_047298557.1:p.Asp692Gly
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#.

2 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss290219515 Jan 12, 2011 (133)
2 ILLUMINA ss3726674872 Jul 13, 2019 (153)
3 ALFA NC_000023.11 - 41542717 Apr 27, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
14356628009, ss290219515, ss3726674872 NC_000023.11:41542716:T:C NC_000023.11:41542716: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.

1 citation for rs137852818
PMID Title Author Year Journal
19377476 A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Tarpey PS et al. 2009 Nature 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