ClinVar Genomic variation as it relates to human health
NM_000388.4(CASR):c.2956G>T (p.Ala986Ser)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000388.4(CASR):c.2956G>T (p.Ala986Ser)
Variation ID: 8349 Accession: VCV000008349.31
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3q21.1 3: 122284910 (GRCh38) [ NCBI UCSC ] 3: 122003757 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 28, 2015 Sep 29, 2024 Feb 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000388.4:c.2956G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000379.3:p.Ala986Ser missense NM_001178065.2:c.2986G>T NP_001171536.2:p.Ala996Ser missense NC_000003.12:g.122284910G>T NC_000003.11:g.122003757G>T NG_009058.2:g.106243G>T NP_000379.2:p.Ala986Ser - Protein change
- A986S, A996S
- Other names
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- Canonical SPDI
- NC_000003.12:122284909:G:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.09425 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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1000 Genomes Project 30x 0.09135
1000 Genomes Project 0.09425
Trans-Omics for Precision Medicine (TOPMed) 0.10436
The Genome Aggregation Database (gnomAD) 0.10682
Exome Aggregation Consortium (ExAC) 0.12693
The Genome Aggregation Database (gnomAD), exomes 0.12850
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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CASR | No evidence available | No evidence available |
GRCh38 GRCh37 |
2735 | 2758 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Serum calcium level
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association (1) |
no assertion criteria provided
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Jul 25, 2018 | RCV000008854.13 |
Benign (8) |
criteria provided, multiple submitters, no conflicts
|
Dec 21, 2017 | RCV000152933.30 | |
Benign (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV000299158.13 | |
Benign (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV000356249.13 | |
Benign (1) |
criteria provided, single submitter
|
Apr 27, 2017 | RCV000343555.13 | |
Benign (1) |
criteria provided, single submitter
|
Apr 27, 2017 | RCV000405678.13 | |
Benign (1) |
no assertion criteria provided
|
- | RCV001269361.9 | |
Benign (1) |
criteria provided, single submitter
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Feb 1, 2024 | RCV001510800.15 | |
Benign (1) |
criteria provided, single submitter
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Aug 30, 2018 | RCV004018599.1 | |
Benign (1) |
criteria provided, single submitter
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- | RCV004715641.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Benign
(-)
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criteria provided, single submitter
Method: clinical testing
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NOT SPECIFIED
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV000306963.1
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
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Benign
(Apr 07, 2014)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000202363.7
First in ClinVar: Jan 29, 2015 Last updated: Apr 09, 2018 |
Number of individuals with the variant: 2
Sex: mixed
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Benign
(Jun 05, 2017)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000711769.1
First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
Comment:
p.Ala996Ser in exon 7 of CASR: This variant is not expected to have clinical sig nificance because it has been identified in 19.5% (3223/16508) of … (more)
p.Ala996Ser in exon 7 of CASR: This variant is not expected to have clinical sig nificance because it has been identified in 19.5% (3223/16508) of South Asian ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs1801725). (less)
Number of individuals with the variant: 1
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Benign
(Feb 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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Familial hypocalciuric hypercalcemia
Autosomal dominant hypocalcemia 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001717931.4
First in ClinVar: Jun 15, 2021 Last updated: Feb 28, 2024 |
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Benign
(-)
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criteria provided, single submitter
Method: not provided
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005303517.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
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Benign
(Jul 17, 2017)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Athena Diagnostics
Accession: SCV000612667.1
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
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Benign
(Dec 21, 2017)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000512484.4
First in ClinVar: Mar 08, 2017 Last updated: Apr 09, 2018 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
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Benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Autosomal dominant hypocalcemia 1
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000440142.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
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Benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Neonatal severe primary hyperparathyroidism
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000440141.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
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Benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Familial isolated hypoparathyroidism
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000440140.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
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Benign
(Apr 27, 2017)
|
criteria provided, single submitter
Method: clinical testing
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Familial hypocalciuric hypercalcemia 1
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000440139.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. (less)
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Benign
(Aug 30, 2018)
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criteria provided, single submitter
Method: clinical testing
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Nephrolithiasis/nephrocalcinosis
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV001178781.4
First in ClinVar: Mar 16, 2020 Last updated: May 01, 2024 |
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation … (more)
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
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association
(Jul 25, 2018)
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no assertion criteria provided
Method: literature only
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CASR POLYMORPHISM
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000029064.3
First in ClinVar: Apr 04, 2013 Last updated: Jul 28, 2018 |
Comment on evidence:
In female North American cohorts, Cole et al. (1999) and Cole et al. (2001) described an association between serum ionized calcium and a common polymorphism, … (more)
In female North American cohorts, Cole et al. (1999) and Cole et al. (2001) described an association between serum ionized calcium and a common polymorphism, ala986 to ser (A986S), in the cytoplasmic tail of the calcium-sensing receptor. Scillitani et al. (2004) confirmed the association in 377 healthy Italian Caucasian adults (184 men and 193 women). Their results also suggested that 2 neighboring exon 7 polymorphisms were predictive as well. Relative frequency for the minor 986S allele was 24%. Subjects with the AA genotype had significantly lower serum ionized calcium (P = 0.0001) than subjects with 1 or 2 S alleles. (less)
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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Breast Cancer
Affected status: yes
Allele origin:
germline
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Center of Medical Genetics and Primary Health Care
Accession: SCV001448712.1
First in ClinVar: Dec 07, 2020 Last updated: Dec 07, 2020 |
|
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001743934.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001929713.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001954516.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Polymorphisms in CaSR and CLDN14 Genes Associated with Increased Risk of Kidney Stone Disease in Patients from the Eastern Part of India. | Guha M | PloS one | 2015 | PMID: 26107257 |
The G allele of CaSR R990G polymorphism increases susceptibility to urolithiasis and hypercalciuria: evidences from a comprehensive meta-analysis. | Liu K | BioMed research international | 2015 | PMID: 25705702 |
Effects of the calcium-sensing receptor A986S polymorphism on serum calcium and parathyroid hormone levels in healthy individuals: a meta-analysis. | He Y | Gene | 2012 | PMID: 22024717 |
Association between calcium-sensing receptor gene polymorphisms and recurrent calcium kidney stone disease: a comprehensive gene analysis. | Shakhssalim N | Scandinavian journal of urology and nephrology | 2010 | PMID: 20602573 |
Neonatal hypercalcemia due to polymorphisms of the calcium sensing receptor. | Jack MM | Journal of pediatric endocrinology & metabolism : JPEM | 2009 | PMID: 19694204 |
Association between calcium sensing receptor gene polymorphisms and chronic pancreatitis in a US population: role of serine protease inhibitor Kazal 1type and alcohol. | Muddana V | World journal of gastroenterology | 2008 | PMID: 18680227 |
Hypercalcaemic and hypocalcaemic conditions due to calcium-sensing receptor mutations. | Egbuna OI | Best practice & research. Clinical rheumatology | 2008 | PMID: 18328986 |
Molecular genetic analysis of the calcium sensing receptor gene in patients clinically suspected to have familial hypocalciuric hypercalcemia: phenotypic variation and mutation spectrum in a Danish population. | Nissen PH | The Journal of clinical endocrinology and metabolism | 2007 | PMID: 17698911 |
Neonatal severe hyperparathyroidism associated with a novel de novo heterozygous R551K inactivating mutation and a heterozygous A986S polymorphism of the calcium-sensing receptor gene. | Tõke J | Clinical endocrinology | 2007 | PMID: 17555508 |
R990G polymorphism of calcium-sensing receptor does produce a gain-of-function and predispose to primary hypercalciuria. | Vezzoli G | Kidney international | 2007 | PMID: 17332735 |
Genetic variation at the calcium-sensing receptor (CASR) locus: implications for clinical molecular diagnostics. | Yun FH | Clinical biochemistry | 2007 | PMID: 17320849 |
Interaction between birthweight and polymorphism in the calcium-sensing receptor gene in determination of adult bone mass: the Hertfordshire cohort study. | Lips MA | The Journal of rheumatology | 2007 | PMID: 17309124 |
Primary hyperparathyroidism and the presence of kidney stones are associated with different haplotypes of the calcium-sensing receptor. | Scillitani A | The Journal of clinical endocrinology and metabolism | 2007 | PMID: 17018660 |
The calcium-sensing receptor and related diseases. | D'Souza-Li L | Arquivos brasileiros de endocrinologia e metabologia | 2006 | PMID: 17117288 |
Mutations in the calcium-sensing receptor: a new genetic risk factor for chronic pancreatitis? | Felderbauer P | Scandinavian journal of gastroenterology | 2006 | PMID: 16497624 |
Calcium-sensing receptor gene polymorphism Arg990Gly and its possible effect on response to cinacalcet HCl. | Rothe HM | Pharmacogenetics and genomics | 2005 | PMID: 15864123 |
Blood ionized calcium is associated with clustered polymorphisms in the carboxyl-terminal tail of the calcium-sensing receptor. | Scillitani A | The Journal of clinical endocrinology and metabolism | 2004 | PMID: 15531522 |
Vitamin D receptor, oestrogen receptor-alpha and calcium-sensing receptor genotypes, bone mineral density and biochemical markers in Paget's disease of bone. | Donáth J | Rheumatology (Oxford, England) | 2004 | PMID: 14997007 |
Calcium-sensing receptor gene polymorphism A986S does not predict serum calcium level, bone mineral density, calcaneal ultrasound indices, or fracture rate in a large cohort of elderly women. | Bollerslev J | Calcified tissue international | 2004 | PMID: 14508624 |
Calcium sensing receptor gene A986S polymorphism and responsiveness to calcium supplementation in postmenopausal women. | Young R | The Journal of clinical endocrinology and metabolism | 2003 | PMID: 12574201 |
Influence of calcium-sensing receptor gene on urinary calcium excretion in stone-forming patients. | Vezzoli G | Journal of the American Society of Nephrology : JASN | 2002 | PMID: 12239240 |
Lack of association between calcium-sensing receptor gene "A986S" polymorphism and bone mineral density in Hungarian postmenopausal women. | Takács I | Bone | 2002 | PMID: 12052452 |
Vitamin D and calcium-sensing receptor genotypes in men and premenopausal women with low bone mineral density. | Eckstein M | The Israel Medical Association journal : IMAJ | 2002 | PMID: 12040821 |
Calcium-sensing receptor A986S polymorphism in human rectal cancer. | Speer G | International journal of colorectal disease | 2002 | PMID: 12018449 |
No evidence for point mutations of the calcium-sensing receptor in familial idiopathic hypercalciuria. | Lerolle N | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2001 | PMID: 11733622 |
Frequency of the calcium-sensing receptor variant A986S in patients with primary hyperparathyroidism. | Miedlich S | European journal of endocrinology | 2001 | PMID: 11580999 |
Calcium sensing receptor gene polymorphism, circulating calcium concentrations and bone mineral density in healthy adolescent girls. | Lorentzon M | European journal of endocrinology | 2001 | PMID: 11248745 |
Association between total serum calcium and the A986S polymorphism of the calcium-sensing receptor gene. | Cole DE | Molecular genetics and metabolism | 2001 | PMID: 11161843 |
Molecular variations in the calcium-sensing receptor in relation to sodium balance and presence of hypertension in blacks and whites. | Pratt JH | American journal of hypertension | 2000 | PMID: 10912749 |
A986S polymorphism of calcium-sensing receptor. | Kanazawa H | Lancet (London, England) | 1999 | PMID: 10217111 |
A986S polymorphism of the calcium-sensing receptor and circulating calcium concentrations. | Cole DE | Lancet (London, England) | 1999 | PMID: 10023897 |
Clustered inactivating mutations and benign polymorphisms of the calcium receptor gene in familial benign hypocalciuric hypercalcemia suggest receptor functional domains. | Heath H 3rd | The Journal of clinical endocrinology and metabolism | 1996 | PMID: 8636323 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CASR | - | - | - | - |
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Text-mined citations for rs1801725 ...
HelpRecord last updated Nov 25, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.