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NM_004320.5(ATP2A1):c.2536G>A (p.Ala846Thr) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 7, 2017
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:
RCV000498261.1

Allele description

NM_004320.5(ATP2A1):c.2536G>A (p.Ala846Thr)

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_004320.5(ATP2A1):c.2536G>A (p.Ala846Thr)
HGVS:
  • NC_000016.10:g.28902591G>A
  • NG_023327.1:g.29104G>A
  • NM_001286075.1:c.2161G>A
  • NM_004320.5:c.2536G>A
  • NM_173201.4:c.2536G>A
  • NP_001273004.1:p.Ala721Thr
  • NP_004311.1:p.Ala846Thr
  • NP_775293.1:p.Ala846Thr
  • NC_000016.9:g.28913912G>A
  • NM_004320.4:c.2536G>A
  • NM_173201.3:c.2536G>A
Protein change:
A721T
Links:
dbSNP: rs186012808
NCBI 1000 Genomes Browser:
rs186012808
Molecular consequence:
  • NM_001286075.1:c.2161G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004320.5:c.2536G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173201.4:c.2536G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000589404GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jun 7, 2017) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000589404.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the ATP2A1 gene. The A846T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A846T variant is observed in 52/66314 (0.1%) alleles from individuals of European background, including 1 homozygous individual in the ExAC dataset (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A846T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 15, 2021