NM_000388.4(CASR):c.3062C>G (p.Thr1021Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 8, 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:: RCV001864120.7

Allele description [Variation Report for NM_000388.4(CASR):c.3062C>G (p.Thr1021Arg)]

NM_000388.4(CASR):c.3062C>G (p.Thr1021Arg)

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.3062C>G (p.Thr1021Arg)

HGVS:

NC_000003.12:g.122285016C>G
NG_009058.2:g.106349C>G
NM_000388.3:c.3062C>G
NM_000388.4:c.3062C>GMANE SELECT
NM_001178065.2:c.3092C>G
NP_000379.3:p.Thr1021Arg
NP_001171536.2:p.Thr1031Arg
NC_000003.11:g.122003863C>G
NG_009058.1:g.106334C>G

Protein change:

T1021R

Links:

dbSNP: rs759009566

NCBI 1000 Genomes Browser:

rs759009566

Molecular consequence:

NM_000388.4:c.3062C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001178065.2:c.3092C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial hypocalciuric hypercalcemia (FHH)
Synonyms:: Familial benign hypercalcemia
Identifiers:: MONDO: MONDO:0018458; MedGen: C1809471; OMIM: PS145980

Name:: Autosomal dominant hypocalcemia 1 (HYPOC1)
Synonyms:: HYPOCALCEMIA, FAMILIAL
Identifiers:: MONDO: MONDO:0011013; MedGen: C0342345; OMIM: 601198

Recent activity

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phosducin, partial [Voeltzkowia yamagishii]
phosducin, partial [Voeltzkowia yamagishii]
gi|815860098|gb|AKE49021.1|

Protein
RecName: Full=Triosephosphate isomerase; Short=TIM; AltName: Full=Triose-phospha...
RecName: Full=Triosephosphate isomerase; Short=TIM; AltName: Full=Triose-phosphate isomerase
gi|1351275|sp|P48499.1|TPIS_LEIME

Protein
Lambdapapillomavirus
Lambdapapillomavirus
A genus of DNA viruses in the family papillomaviridae, causing mucosal and cutaneous lesions in cats and dogs. Canine oral papillomavirus is the type species....<br/>Year introduced: 2007

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002118821	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 8, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002118821

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 8, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002118821.3

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

Description

This sequence change replaces threonine, which is neutral and polar, with arginine, which is basic and polar, at codon 1021 of the CASR protein (p.Thr1021Arg). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with CASR-related conditions. ClinVar contains an entry for this variant (Variation ID: 1358593). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

ClinVar

Relating variation to medicine