NM_001232.4(CASQ2):c.80C>T (p.Thr27Ile) AND not specified

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Aug 3, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000825714.13

Allele description [Variation Report for NM_001232.4(CASQ2):c.80C>T (p.Thr27Ile)]

NM_001232.4(CASQ2):c.80C>T (p.Thr27Ile)

Gene:

CASQ2:calsequestrin 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p13.1

Genomic location:

Preferred name:

NM_001232.4(CASQ2):c.80C>T (p.Thr27Ile)

HGVS:

NC_000001.11:g.115768462G>A
NG_008802.1:g.5344C>T
NM_001232.4:c.80C>TMANE SELECT
NP_001223.2:p.Thr27Ile
NP_001223.2:p.Thr27Ile
LRG_404t1:c.80C>T
LRG_404:g.5344C>T
LRG_404p1:p.Thr27Ile
NC_000001.10:g.116311083G>A
NM_001232.3:c.80C>T
p.Thr27Ile

Protein change:

T27I

Links:

dbSNP: rs773237428

NCBI 1000 Genomes Browser:

rs773237428

Molecular consequence:

NM_001232.4:c.80C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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PRAME family member 9 [Homo sapiens]
PRAME family member 9 [Homo sapiens]
gi|611434972|ref|NP_001010890.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000967163	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Oct 24, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005381458	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Aug 3, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000967163

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Oct 24, 2018)

germline

clinical testing

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

SCV005381458

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Aug 3, 2024)

germline

clinical testing

Citation Link

Help

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
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000967163.1

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

Description

The p.Thr27Ile variant in CASQ2 is classified as likely benign due to a lack of conservation across species. 5 mammals (guinea pig, chinchilla, camel, alpaca, m anatee) carry an Isoleucine (Ile) at this position despite high nearby amino aci d conservation. It has been identified in 5/251286 chromosomes by gnomAD (http:/ /gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BP4_Strong.

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005381458.1

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

#	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: Nov 3, 2024

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