NM_000053.4(ATP7B):c.3247C>T (p.Leu1083Phe) AND Wilson disease

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Aug 10, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000586978.4

Allele description [Variation Report for NM_000053.4(ATP7B):c.3247C>T (p.Leu1083Phe)]

NM_000053.4(ATP7B):c.3247C>T (p.Leu1083Phe)

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.3247C>T (p.Leu1083Phe)
HGVS:
  • NC_000013.11:g.51942551G>A
  • NG_008806.1:g.73944C>T
  • NM_000053.4:c.3247C>TMANE SELECT
  • NM_001005918.3:c.2626C>T
  • NM_001243182.2:c.2914C>T
  • NM_001330578.2:c.3013C>T
  • NM_001330579.2:c.2995C>T
  • NP_000044.2:p.Leu1083Phe
  • NP_001005918.1:p.Leu876Phe
  • NP_001230111.1:p.Leu972Phe
  • NP_001317507.1:p.Leu1005Phe
  • NP_001317508.1:p.Leu999Phe
  • NC_000013.10:g.52516687G>A
  • NM_000053.2:c.3247C>T
Protein change:
L1005F
Links:
dbSNP: rs1286080173
NCBI 1000 Genomes Browser:
rs1286080173
Molecular consequence:
  • NM_000053.4:c.3247C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005918.3:c.2626C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243182.2:c.2914C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330578.2:c.3013C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330579.2:c.2995C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000694441Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Pathogenic
(Nov 21, 2016)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001132129Counsylno assertion criteria providedLikely pathogenic
(Jun 27, 2019)
unknownclinical testing

PubMed (9)
[See all records that cite these PMIDs]

SCV001455592Natera, Inc.no assertion criteria providedPathogenic
(Sep 16, 2020)
germlineclinical testing

SCV001977262Nilou-Genome Labcriteria provided, single submitter
Likely pathogenic
(Aug 10, 2021)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Pseudo-dominant inheritance in Wilson's disease.

Park H, Park DK, Kim MS, Yoon JH.

Neurol Sci. 2016 Jan;37(1):153-155. doi: 10.1007/s10072-015-2394-8. Epub 2015 Oct 14. No abstract available.

PubMed [citation]
PMID:
26466587

Diverse functional properties of Wilson disease ATP7B variants.

Huster D, Kühne A, Bhattacharjee A, Raines L, Jantsch V, Noe J, Schirrmeister W, Sommerer I, Sabri O, Berr F, Mössner J, Stieger B, Caca K, Lutsenko S.

Gastroenterology. 2012 Apr;142(4):947-956.e5. doi: 10.1053/j.gastro.2011.12.048. Epub 2012 Jan 10.

PubMed [citation]
PMID:
22240481
PMCID:
PMC3461965
See all PubMed Citations (10)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694441.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Variant summary: The ATP7B c.3247C>T (p.Leu1083Phe) variant involves the alteration of a conserved nucleotide. 4/5 in silico tools predict a damaging outcome for this variant. This variant is absent in 120420 control chromosomes but was reported at high frequency in Korean WD patients, and also in Japanese WD patients. Functionally, the variant was shown to lead to significant abnormalities subcellular localization and protein level. Taken together, this variant is classified as pathogenic.

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

From Counsyl, SCV001132129.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001455592.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Nilou-Genome Lab, SCV001977262.1

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

Last Updated: Nov 27, 2021

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