NM_170665.4(ATP2A2):c.2058del (p.Ile686fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 15, 2016
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:: RCV000342838.1

Allele description [Variation Report for NM_170665.4(ATP2A2):c.2058del (p.Ile686fs)]

NM_170665.4(ATP2A2):c.2058del (p.Ile686fs)

Genes:

ATP2A2:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 [Gene - OMIM - HGNC]
LOC126861637:MED14-independent group 3 enhancer GRCh37_chr12:110778306-110779505 [Gene]

Variant type:

Deletion

Cytogenetic location:

12q24.11

Genomic location:

Preferred name:

NM_170665.4(ATP2A2):c.2058del (p.Ile686fs)

HGVS:

NC_000012.12:g.110340955del
NG_007097.2:g.64329del
NM_001681.4:c.2058del
NM_170665.4:c.2058delMANE SELECT
NP_001672.1:p.Ile686fs
NP_733765.1:p.Ile686fs
NC_000012.11:g.110778760del
NM_170665.3:c.2058delC

Protein change:

I686fs

Links:

dbSNP: rs886041576

NCBI 1000 Genomes Browser:

rs886041576

Molecular consequence:

NM_001681.4:c.2058del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_170665.4:c.2058del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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reticulocalbin-3 precursor [Mus musculus]
reticulocalbin-3 precursor [Mus musculus]
gi|188035858|ref|NP_080831.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000330260	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Feb 15, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000330260

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Feb 15, 2016)

germline

clinical testing

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000330260.5

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

Description

The c.2058delC pathogenic variant in the ATP2A2 gene causes a frameshift starting with codon Isoleucine 686, changes this amino acid to a Methionine residue and creates a premature Stop codon at position 2 of the new reading frame, denoted p.Ile686MetfsX2. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In addition, c.2058delC was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Although this variant has not been previously reported to our knowledge, we consider it to be pathogenic.

#	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		not provided	not provided	not provided	not provided

Last Updated: Mar 26, 2023

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