NM_000388.4(CASR):c.2237C>T (p.Ala746Val) AND Nephrolithiasis/nephrocalcinosis

Germline classification:: Likely benign (1 submission)
Last evaluated:: Feb 23, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004023948.1

Allele description [Variation Report for NM_000388.4(CASR):c.2237C>T (p.Ala746Val)]

NM_000388.4(CASR):c.2237C>T (p.Ala746Val)

Gene:

CASR:calcium sensing receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q21.1

Genomic location:

Preferred name:

NM_000388.4(CASR):c.2237C>T (p.Ala746Val)

HGVS:

NC_000003.12:g.122284191C>T
NG_009058.1:g.105509C>T
NM_000388.4:c.2237C>TMANE SELECT
NM_001178065.1:c.2267C>T
NM_001178065.2:c.2267C>T
NP_000379.3:p.Ala746Val
NP_001171536.2:p.Ala756Val
NC_000003.11:g.122003038C>T
NM_000388.3:c.2237C>T

Protein change:

A746V

Links:

dbSNP: rs139417576

NCBI 1000 Genomes Browser:

rs139417576

Molecular consequence:

NM_000388.4:c.2237C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001178065.2:c.2267C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Nephrolithiasis/nephrocalcinosis
Identifiers:: MedGen: CN580796

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hypothetical protein FLJ12892 [Homo sapiens]
hypothetical protein FLJ12892 [Homo sapiens]
gi|31377713|ref|NP_073594.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002727925	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Feb 23, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26963950, 31672324 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002727925

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Feb 23, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Familial Hypocalciuric Hypercalcemia Types 1 and 3 and Primary Hyperparathyroidism: Similarities and Differences.

Vargas-Poussou R, Mansour-Hendili L, Baron S, Bertocchio JP, Travers C, Simian C, Treard C, Baudouin V, Beltran S, Broux F, Camard O, Cloarec S, Cormier C, Debussche X, Dubosclard E, Eid C, Haymann JP, Kiando SR, Kuhn JM, Lefort G, Linglart A, Lucas-Pouliquen B, et al.

J Clin Endocrinol Metab. 2016 May;101(5):2185-95. doi: 10.1210/jc.2015-3442. Epub 2016 Mar 10.

PubMed [citation]

PMID:: 26963950

High-throughput sequencing contributes to the diagnosis of tubulopathies and familial hypercalcemia hypocalciuria in adults.

Hureaux M, Ashton E, Dahan K, Houillier P, Blanchard A, Cormier C, Koumakis E, Iancu D, Belge H, Hilbert P, Rotthier A, Del Favero J, Schaefer F, Kleta R, Bockenhauer D, Jeunemaitre X, Devuyst O, Walsh SB, Vargas-Poussou R.

Kidney Int. 2019 Dec;96(6):1408-1416. doi: 10.1016/j.kint.2019.08.027. Epub 2019 Sep 16.

PubMed [citation]

PMID:: 31672324

Details of each submission

From Ambry Genetics, SCV002727925.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as likely 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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