NM_170665.4(ATP2A2):c.1910G>A (p.Arg637His) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Dec 4, 2023
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:: RCV003489703.1

Allele description [Variation Report for NM_170665.4(ATP2A2):c.1910G>A (p.Arg637His)]

NM_170665.4(ATP2A2):c.1910G>A (p.Arg637His)

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:

single nucleotide variant

Cytogenetic location:

12q24.11

Genomic location:

Preferred name:

NM_170665.4(ATP2A2):c.1910G>A (p.Arg637His)

HGVS:

NC_000012.12:g.110340807G>A
NG_007097.2:g.64181G>A
NG_086135.1:g.407G>A
NM_001413013.1:c.1805G>A
NM_001413014.1:c.1910G>A
NM_001413015.1:c.1535G>A
NM_001681.4:c.1910G>A
NM_170665.4:c.1910G>AMANE SELECT
NP_001399942.1:p.Arg602His
NP_001399943.1:p.Arg637His
NP_001399944.1:p.Arg512His
NP_001672.1:p.Arg637His
NP_733765.1:p.Arg637His
NC_000012.11:g.110778612G>A

Protein change:

R512H

Molecular consequence:

NM_001413013.1:c.1805G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413014.1:c.1910G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413015.1:c.1535G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001681.4:c.1910G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_170665.4:c.1910G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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PTSG_07914 [Salpingoeca rosetta]
PTSG_07914 [Salpingoeca rosetta]
Gene ID:16072276

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004241801	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Dec 4, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004241801

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Dec 4, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004241801.1

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

Description

Variant summary: ATP2A2 c.1910G>A (p.Arg637His) results in a non-conservative amino acid change located in the P-type ATPase, haloacid dehalogenase domain (IPR044492) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.5e-05 in 1,614,092 control chromosomes (i.e. in 41 heterozygous individuals), predominantly at a frequency of 0.00013 within the South Asian subpopulation in the gnomAD database (v.4.0 dataset). This frequency suggests that the variant is not associated with a highly penetrant, early onset dominant condition, and thus could be a benign polymorphism. To our knowledge, no occurrence of c.1910G>A in individuals affected with ATP2A2-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely benign.

#	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: Feb 14, 2024

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