NM_145046.5(CALR3):c.697C>G (p.Leu233Val) AND Hypertrophic cardiomyopathy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 2020
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:: RCV001281573.2

Allele description [Variation Report for NM_145046.5(CALR3):c.697C>G (p.Leu233Val)]

NM_145046.5(CALR3):c.697C>G (p.Leu233Val)

Gene:

CALR3:calreticulin 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.11

Genomic location:

Preferred name:

NM_145046.5(CALR3):c.697C>G (p.Leu233Val)

HGVS:

NC_000019.10:g.16482767G>C
NG_031959.2:g.150438C>G
NM_145046.5:c.697C>GMANE SELECT
NP_659483.2:p.Leu233Val
LRG_422t1:c.697C>G
LRG_422:g.150438C>G
NC_000019.9:g.16593578G>C
NM_145046.4:c.697C>G

Protein change:

L233V

Links:

dbSNP: rs2093383229

NCBI 1000 Genomes Browser:

rs2093383229

Molecular consequence:

NM_145046.5:c.697C>G - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

Uncertain function

Observations:

Condition(s)

Name:: Hypertrophic cardiomyopathy
Synonyms:: HYPERTROPHIC MYOCARDIOPATHY
Identifiers:: MONDO: MONDO:0005045; MeSH: D002312; MedGen: C0007194; Human Phenotype Ontology: HP:0001639

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001432806	Molecular Genetics Lab, DMCH Ludhiana, Dayanand Medical College & Hospital (DMCH)	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 22, 2020)	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

SCV001432806

Molecular Genetics Lab, DMCH Ludhiana, Dayanand Medical College & Hospital (DMCH)

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 22, 2020)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
North Indian	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Molecular Genetics Lab, DMCH Ludhiana, Dayanand Medical College & Hospital (DMCH), SCV001432806.1

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

Description

The missense variant p.L233V in CALR3 (NM_145046.4) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.L233V variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. There is a small physicochemical difference between leucine and valine, which is not likely to impact secondary protein structure as these residues share similar properties. In silico predictors are contradictory (SIFT-Tolerated, Polyphen-2damaging). The residue is conserved across species. For these reasons, this variant has been classified as Uncertain Significance.

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

Last Updated: Jun 23, 2024

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