NM_170665.4(ATP2A2):c.2407G>A (p.Ala803Thr) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 9, 2022
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:: RCV003062550.3

Allele description [Variation Report for NM_170665.4(ATP2A2):c.2407G>A (p.Ala803Thr)]

NM_170665.4(ATP2A2):c.2407G>A (p.Ala803Thr)

Gene:

ATP2A2:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.11

Genomic location:

Preferred name:

NM_170665.4(ATP2A2):c.2407G>A (p.Ala803Thr)

HGVS:

NC_000012.12:g.110343320G>A
NG_007097.2:g.66694G>A
NM_001413013.1:c.2302G>A
NM_001413014.1:c.2407G>A
NM_001413015.1:c.2032G>A
NM_001681.4:c.2407G>A
NM_170665.4:c.2407G>AMANE SELECT
NP_001399942.1:p.Ala768Thr
NP_001399943.1:p.Ala803Thr
NP_001399944.1:p.Ala678Thr
NP_001672.1:p.Ala803Thr
NP_733765.1:p.Ala803Thr
NC_000012.11:g.110781125G>A

Protein change:

A678T

Molecular consequence:

NM_001413013.1:c.2302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413014.1:c.2407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413015.1:c.2032G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001681.4:c.2407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_170665.4:c.2407G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003441085	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 9, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10441323, 16766529, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003441085

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 9, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

Spectrum of novel ATP2A2 mutations in patients with Darier's disease.

Sakuntabhai A, Burge S, Monk S, Hovnanian A.

Hum Mol Genet. 1999 Sep;8(9):1611-9.

PubMed [citation]

PMID:: 10441323

Comprehensive analysis of expression and function of 51 sarco(endo)plasmic reticulum Ca2+-ATPase mutants associated with Darier disease.

Miyauchi Y, Daiho T, Yamasaki K, Takahashi H, Ishida-Yamamoto A, Danko S, Suzuki H, Iizuka H.

J Biol Chem. 2006 Aug 11;281(32):22882-95. Epub 2006 Jun 9.

PubMed [citation]

PMID:: 16766529

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003441085.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This missense change has been observed in individuals with Darier disease (PMID: 10441323; Invitae). It has also been observed to segregate with disease in related individuals. For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects ATP2A2 function (PMID: 16766529). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ATP2A2 protein function. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 803 of the ATP2A2 protein (p.Ala803Thr).

#	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: Sep 29, 2024

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