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NM_000388.4(CASR):c.3117C>T (p.Asp1039=) AND Nephrolithiasis/nephrocalcinosis

Germline classification:
Likely benign (1 submission)
Last evaluated:
Nov 16, 2021
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:
RCV004048383.1

Allele description [Variation Report for NM_000388.4(CASR):c.3117C>T (p.Asp1039=)]

NM_000388.4(CASR):c.3117C>T (p.Asp1039=)

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.3117C>T (p.Asp1039=)
HGVS:
  • NC_000003.12:g.122285071C>T
  • NG_009058.2:g.106404C>T
  • NM_000388.4:c.3117C>TMANE SELECT
  • NM_001178065.2:c.3147C>T
  • NP_000379.3:p.Asp1039=
  • NP_001171536.2:p.Asp1049=
  • NC_000003.11:g.122003918C>T
  • NM_000388.3:c.3117C>T
Molecular consequence:
  • NM_000388.4:c.3117C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001178065.2:c.3147C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Nephrolithiasis/nephrocalcinosis
Identifiers:
MedGen: CN580796

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002607476Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Nov 16, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002607476.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024