NM_000053.4(ATP7B):c.2428G>T (p.Glu810Ter) AND Wilson disease

Clinical significance:Likely pathogenic (Last evaluated: Sep 7, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000670601.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.2428G>T (p.Glu810Ter)]

NM_000053.4(ATP7B):c.2428G>T (p.Glu810Ter)

Gene:
ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q14.3
Genomic location:
Preferred name:
NM_000053.4(ATP7B):c.2428G>T (p.Glu810Ter)
HGVS:
  • NC_000013.11:g.51957535C>A
  • NG_008806.1:g.58960G>T
  • NM_000053.4:c.2428G>TMANE SELECT
  • NM_001005918.3:c.1942G>T
  • NM_001243182.2:c.2095G>T
  • NM_001330578.2:c.2194G>T
  • NM_001330579.2:c.2176G>T
  • NP_000044.2:p.Glu810Ter
  • NP_001005918.1:p.Glu648Ter
  • NP_001230111.1:p.Glu699Ter
  • NP_001317507.1:p.Glu732Ter
  • NP_001317508.1:p.Glu726Ter
  • NC_000013.10:g.52531671C>A
  • NM_000053.3:c.2428G>T
Protein change:
E648*
Links:
dbSNP: rs770020484
NCBI 1000 Genomes Browser:
rs770020484
Molecular consequence:
  • NM_000053.4:c.2428G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001005918.3:c.1942G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001243182.2:c.2095G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001330578.2:c.2194G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001330579.2:c.2176G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Wilson disease (WND)
Synonyms:
Wilson's disease; Hepatolenticular degeneration
Identifiers:
MONDO: MONDO:0010200; MedGen: C0019202; Orphanet: 905; OMIM: 277900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000795473Counsylcriteria provided, single submitter
Likely pathogenic
(Nov 8, 2017)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000918602Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(Sep 7, 2018)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Summary from all submissions

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

Citations

PubMed

Molecular analysis of Wilson patients: direct sequencing and MLPA analysis in the ATP7B gene and Atox1 and COMMD1 gene analysis.

Bost M, Piguet-Lacroix G, Parant F, Wilson CM.

J Trace Elem Med Biol. 2012 Jun;26(2-3):97-101. doi: 10.1016/j.jtemb.2012.04.024. Epub 2012 Jun 5.

PubMed [citation]
PMID:
22677543

Details of each submission

From Counsyl, SCV000795473.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918602.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: ATP7B c.2428G>T (p.Glu810X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 246246 control chromosomes (gnomAD). c.2428G>T has been reported in the literature in individuals affected with Wilson Disease (Bost_2012). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submission from another clinical diagnostic laboratory (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Nov 27, 2021

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