NM_004320.6(ATP2A1):c.2077T>G (p.Ser693Ala) AND Brody myopathy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 31, 2021
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:: RCV000525672.6

Allele description [Variation Report for NM_004320.6(ATP2A1):c.2077T>G (p.Ser693Ala)]

NM_004320.6(ATP2A1):c.2077T>G (p.Ser693Ala)

Gene:

ATP2A1:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

NM_004320.6(ATP2A1):c.2077T>G (p.Ser693Ala)

HGVS:

NC_000016.10:g.28900893T>G
NG_023327.1:g.27406T>G
NM_001286075.2:c.1702T>G
NM_004320.6:c.2077T>GMANE SELECT
NM_173201.5:c.2077T>G
NP_001273004.1:p.Ser568Ala
NP_004311.1:p.Ser693Ala
NP_775293.1:p.Ser693Ala
NC_000016.9:g.28912214T>G
NM_173201.3:c.2077T>G

Protein change:

S568A

Links:

dbSNP: rs563510255

NCBI 1000 Genomes Browser:

rs563510255

Molecular consequence:

NM_001286075.2:c.1702T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004320.6:c.2077T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_173201.5:c.2077T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Brody myopathy
Synonyms:: BRODY DISEASE
Identifiers:: MONDO: MONDO:0010977; MedGen: C1832918; Orphanet: 53347; OMIM: 601003

Recent activity

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brother of CDO isoform 1 precursor [Homo sapiens]
brother of CDO isoform 1 precursor [Homo sapiens]
gi|1802446939|ref|NP_001365003.1|

Protein
PREDICTED: Solea senegalensis kirre like nephrin family adhesion molecule 3b (ki...
PREDICTED: Solea senegalensis kirre like nephrin family adhesion molecule 3b (kirrel3b), transcript variant X9, mRNA
gi|2105458185|ref|XM_044032041.1|

Nucleotide
Xylobium pallidiflorum voucher ORDNA00852 maturase K (matK) gene, partial cds; c...
Xylobium pallidiflorum voucher ORDNA00852 maturase K (matK) gene, partial cds; chloroplast
gi|2216788349|gnl|uoguelph|ABGCO918 atK|gb|MT518862.1|

Nucleotide
Arrhythmogenic right ventricular dysplasia 9
Arrhythmogenic right ventricular dysplasia 9

MedGen
"Fibrofatty replacement of right ventricular myocardium"[Clinical... (2)
"Fibrofatty replacement of right ventricular myocardium"[Clinical Features] OR 369873[uid]
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000638287	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 31, 2021)	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

SCV000638287

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 31, 2021)

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
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, SCV000638287.5

#	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 serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 693 of the ATP2A1 protein (p.Ser693Ala). This variant is present in population databases (rs563510255, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ATP2A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 464081). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest 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: Sep 29, 2024

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