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NM_000388.4(CASR):c.1631G>A (p.Arg544Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(5);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000237758.10
Variation ID:
237758
Description:
single nucleotide variant
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NM_000388.4(CASR):c.1631G>A (p.Arg544Gln)

Allele ID
239066
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q21.1
Genomic location
3: 122282135 (GRCh38) GRCh38 UCSC
3: 122000982 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.122000982G>A
NC_000003.12:g.122282135G>A
NG_009058.1:g.103453G>A
... more HGVS
Protein change
R544Q, R554Q
Other names
-
Canonical SPDI
NC_000003.12:122282134:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00073
The Genome Aggregation Database (gnomAD) 0.00083
1000 Genomes Project 0.00020
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00108
Links
ClinGen: CA2569716
dbSNP: rs115230894
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Apr 14, 2017 RCV000727289.4
Likely benign 1 criteria provided, single submitter - RCV000251515.3
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000281394.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000312098.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000337880.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000390791.4
Uncertain significance 1 criteria provided, single submitter Dec 3, 2018 RCV001012502.1
Benign 1 criteria provided, single submitter Dec 7, 2020 RCV001081459.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CASR No evidence available No evidence available GRCh38
GRCh37
1295 1313

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000306958.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Hypocalcemia, autosomal dominant 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000440095.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Neonatal severe hyperparathyroidism
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000440097.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Familial isolated hypoparathyroidism
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000440098.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Hypocalciuric hypercalcemia, familial, type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000440096.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hypocalciuric hypercalcemia
Hypocalcemia, autosomal dominant 1
Allele origin: germline
Invitae
Accession: SCV000284783.7
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Apr 14, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000707277.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Mar 21, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000581748.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R544Q variant previously has been reported previously as a rare variant in association with familial hypocalciuric hypercalcemia (FHH) (Nissen et al., 2012). It is … (more)
Uncertain significance
(Dec 03, 2018)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV001172962.2
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (2)
Comment:
The p.R544Q variant (also known as c.1631G>A), located in coding exon 5 of the CASR gene, results from a G to A substitution at nucleotide … (more)

Functional evidence

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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 this variant

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Title Author Journal Year Link
Homozygous Calcium-Sensing Receptor Polymorphism R544Q Presents as Hypocalcemic Hypoparathyroidism. Cavaco BM The Journal of clinical endocrinology and metabolism 2018 PMID: 29846619
Identification of rare and frequent variants of the CASR gene by high-resolution melting. Nissen PH Clinica chimica acta; international journal of clinical chemistry 2012 PMID: 22192860
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CASR - - - -

Text-mined citations for rs115230894...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 06, 2021