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NM_000052.7(ATP7A):c.1954C>T (p.Arg652Trp) AND Inborn genetic diseases

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 6, 2020
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:
RCV002416121.2

Allele description [Variation Report for NM_000052.7(ATP7A):c.1954C>T (p.Arg652Trp)]

NM_000052.7(ATP7A):c.1954C>T (p.Arg652Trp)

Gene:
ATP7A:ATPase copper transporting alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq21.1
Genomic location:
Preferred name:
NM_000052.7(ATP7A):c.1954C>T (p.Arg652Trp)
HGVS:
  • NC_000023.11:g.78011456C>T
  • NG_013224.2:g.105760C>T
  • NM_000052.7:c.1954C>TMANE SELECT
  • NM_001282224.2:c.1954C>T
  • NP_000043.4:p.Arg652Trp
  • NP_001269153.1:p.Arg652Trp
  • NC_000023.10:g.77266953C>T
  • NM_000052.4:c.1954C>T
  • NM_000052.6:c.1954C>T
Protein change:
R652W
Links:
dbSNP: rs377714939
NCBI 1000 Genomes Browser:
rs377714939
Molecular consequence:
  • NM_000052.7:c.1954C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282224.2:c.1954C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002718817Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Uncertain significance
(Aug 6, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002718817.2

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

Description

The p.R652W variant (also known as c.1954C>T), located in coding exon 8 of the ATP7A gene, results from a C to T substitution at nucleotide position 1954. The arginine at codon 652 is replaced by tryptophan, an amino acid with dissimilar properties. Based on data from gnomAD, the c.1954C>T variant has an overall frequency of 0.004% (9/204,698) of total alleles studied. The highest observed frequency was 0.02% (4/18,955) in the African sub-population, with no hemizygotes observed. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: May 1, 2024