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dbSNP Short Genetic Variations

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.

rs104893711

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:122284316 (GRCh38.p12) 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=0.0000 (3/78702, PAGE_STUDY)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CASR : Missense Variant
Publications
1 citation
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.p12 chr 3 NC_000003.12:g.122284316T>C
GRCh37.p13 chr 3 NC_000003.11:g.122003163T>C
CASR RefSeqGene NG_009058.1:g.105634T>C
Gene: CASR, calcium sensing receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CASR transcript variant 1 NM_001178065.2:c.2392T>C F [TTC] > L [CTC] Coding Sequence Variant
extracellular calcium-sensing receptor isoform 1 precursor NP_001171536.2:p.Phe798Leu F (Phe) > L (Leu) Missense Variant
CASR transcript variant 2 NM_000388.4:c.2362T>C F [TTC] > L [CTC] Coding Sequence Variant
extracellular calcium-sensing receptor isoform 2 precursor NP_000379.3:p.Phe788Leu F (Phe) > L (Leu) Missense Variant
CASR transcript variant X4 XM_005247837.2:c.1879T>C F [TTC] > L [CTC] Coding Sequence Variant
extracellular calcium-sensing receptor isoform X2 XP_005247894.1:p.Phe627Leu F (Phe) > L (Leu) Missense Variant
CASR transcript variant X1 XM_017007324.1:c.2362T>C F [TTC] > L [CTC] Coding Sequence Variant
extracellular calcium-sensing receptor isoform X1 XP_016862813.1:p.Phe788Leu F (Phe) > L (Leu) Missense Variant
CASR transcript variant X2 XM_006713789.3:c.2362T>C F [TTC] > L [CTC] Coding Sequence Variant
extracellular calcium-sensing receptor isoform X1 XP_006713852.1:p.Phe788Leu F (Phe) > L (Leu) Missense Variant
CASR transcript variant X3 XM_017007325.1:c.2362T>C F [TTC] > L [CTC] Coding Sequence Variant
extracellular calcium-sensing receptor isoform X1 XP_016862814.1:p.Phe788Leu F (Phe) > L (Leu) 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.

Allele: C (allele ID: 23387 )
ClinVar Accession Disease Names Clinical Significance
RCV000008853.6 Hypocalcemia, autosomal dominant 1 Pathogenic
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 PAGE Study Global Study-wide 78702 T=1.0000 C=0.0000
The PAGE Study AfricanAmerican Sub 32516 T=1.0000 C=0.0000
The PAGE Study Mexican Sub 10810 T=0.9999 C=0.0001
The PAGE Study Asian Sub 8318 T=1.000 C=0.000
The PAGE Study PuertoRican Sub 7918 T=1.000 C=0.000
The PAGE Study NativeHawaiian Sub 4534 T=1.000 C=0.000
The PAGE Study Cuban Sub 4230 T=1.000 C=0.000
The PAGE Study Dominican Sub 3828 T=1.000 C=0.000
The PAGE Study CentralAmerican Sub 2450 T=1.000 C=0.000
The PAGE Study SouthAmerican Sub 1982 T=1.000 C=0.000
The PAGE Study NativeAmerican Sub 1260 T=1.000 C=0.000
The PAGE Study SouthAsian Sub 856 T=1.00 C=0.00
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 Note
GRCh38.p12 chr 3 NC_000003.12:g.122284316= NC_000003.12:g.12228431...

NC_000003.12:g.122284316T>C

GRCh37.p13 chr 3 NC_000003.11:g.122003163= NC_000003.11:g.12200316...

NC_000003.11:g.122003163T>C

CASR RefSeqGene NG_009058.1:g.105634= NG_009058.1:g.105634T>C
CASR transcript variant 2 NM_000388.3:c.2362= NM_000388.3:c.2362T>C
CASR transcript variant 2 NM_000388.4:c.2362= NM_000388.4:c.2362T>C
CASR transcript variant 1 NM_001178065.1:c.2392= NM_001178065.1:c.2392T>C
CASR transcript variant 1 NM_001178065.2:c.2392= NM_001178065.2:c.2392T>C
CASR transcript variant X2 XM_006713789.3:c.2362= XM_006713789.3:c.2362T>C
CASR transcript variant X4 XM_005247837.2:c.1879= XM_005247837.2:c.1879T>C
CASR transcript variant X2 XM_005247837.1:c.1879= XM_005247837.1:c.1879T>C
CASR transcript variant X1 XM_017007324.1:c.2362= XM_017007324.1:c.2362T>C
CASR transcript variant X3 XM_017007325.1:c.2362= XM_017007325.1:c.2362T>C
extracellular calcium-sensing receptor isoform 2 precursor NP_000379.3:p.Phe788= NP_000379.3:p.Phe788Leu
extracellular calcium-sensing receptor isoform 1 precursor NP_001171536.2:p.Phe798= NP_001171536.2:p.Phe798Leu
extracellular calcium-sensing receptor isoform X1 XP_006713852.1:p.Phe788= XP_006713852.1:p.Phe788Leu
extracellular calcium-sensing receptor isoform X2 XP_005247894.1:p.Phe627= XP_005247894.1:p.Phe627Leu
extracellular calcium-sensing receptor isoform X1 XP_016862813.1:p.Phe788= XP_016862813.1:p.Phe788Leu
extracellular calcium-sensing receptor isoform X1 XP_016862814.1:p.Phe788= XP_016862814.1:p.Phe788Leu
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#.

7 SubSNP, 1 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244238178 May 28, 2010 (132)
2 OMIM-CURATED-RECORDS ss263193896 Oct 28, 2010 (133)
3 ILLUMINA ss1958599428 Feb 12, 2016 (147)
4 ILLUMINA ss3022279942 Nov 08, 2017 (151)
5 ILLUMINA ss3652758516 Oct 12, 2018 (152)
6 ILLUMINA ss3726051181 Jul 13, 2019 (153)
7 PAGE_CC ss3771059279 Jul 13, 2019 (153)
8 The PAGE Study NC_000003.12 - 122284316 Jul 13, 2019 (153)
9 ClinVar RCV000008853.6 Oct 12, 2018 (152)
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
ss1958599428, ss3022279942, ss3652758516 NC_000003.11:122003162:T:C NC_000003.12:122284315:T:C (self)
RCV000008853.6, 280748, ss244238178, ss263193896, ss3726051181, ss3771059279 NC_000003.12:122284315:T:C NC_000003.12:122284315: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 rs104893711
PMID Title Author Year Journal
12915654 Recurrent familial hypocalcemia due to germline mosaicism for an activating mutation of the calcium-sensing receptor gene. Hendy GN et al. 2003 The Journal of clinical endocrinology and metabolism

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.post246+3cda961