NM_000053.4(ATP7B):c.19_20del (p.Gln7fs) AND Wilson disease

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(2);Pathogenic(1);Uncertain significance(1) (Last evaluated: Aug 10, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000576360.8

Allele description [Variation Report for NM_000053.4(ATP7B):c.19_20del (p.Gln7fs)]

NM_000053.4(ATP7B):c.19_20del (p.Gln7fs)

Gene:
ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q14.3
Genomic location:
Preferred name:
NM_000053.4(ATP7B):c.19_20del (p.Gln7fs)
HGVS:
  • NC_000013.10:g.52585454_52585455del
  • NC_000013.11:g.52011319_52011320del
  • NG_008806.1:g.5176_5177del
  • NG_028038.1:g.3933_3934del
  • NM_000053.4:c.19_20delMANE SELECT
  • NM_001005918.3:c.19_20del
  • NM_001243182.2:c.19_20del
  • NM_001330578.2:c.19_20del
  • NM_001330579.2:c.19_20del
  • NP_000044.2:p.Gln7fs
  • NP_001005918.1:p.Gln7fs
  • NP_001230111.1:p.Gln7fs
  • NP_001317507.1:p.Gln7fs
  • NP_001317508.1:p.Gln7fs
  • NC_000013.10:g.52585454_52585455del
  • NC_000013.10:g.52585455_52585456del
  • NC_000013.10:g.52585455_52585456delGT
  • NM_000053.2:c.19_20del
  • NM_000053.3:c.19_20del
  • NM_000053.3:c.19_20delCA
  • NM_001005918.2:c.19_20delCA
  • p.Gln7fs
Protein change:
Q7fs
Links:
dbSNP: rs749363958
NCBI 1000 Genomes Browser:
rs749363958
Molecular consequence:
  • NM_000053.4:c.19_20del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001005918.3:c.19_20del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001243182.2:c.19_20del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330578.2:c.19_20del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330579.2:c.19_20del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000678019Counsylcriteria provided, single submitter
Uncertain significance
(May 30, 2017)
unknownclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV000939965Invitaecriteria provided, single submitter
Pathogenic
(Sep 19, 2020)
germlineclinical testing

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

SCV001163740Baylor Geneticscriteria provided, single submitter
Likely pathogenicgermlineclinical testing

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

SCV001977202Nilou-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 providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Genotyping microarray as a novel approach for the detection of ATP7B gene mutations in patients with Wilson disease.

Gojová L, Jansová E, Külm M, Pouchlá S, Kozák L.

Clin Genet. 2008 May;73(5):441-52. doi: 10.1111/j.1399-0004.2008.00989.x. Epub 2007 Mar 25.

PubMed [citation]
PMID:
18371106

Wilson's disease in an adult asymptomatic patient: a potential role for modifying factors of copper metabolism.

Loudianos G, Incollu S, Mameli E, Lepori MB.

Ann Gastroenterol. 2016 Jan-Mar;29(1):96-8.

PubMed [citation]
PMID:
26752957
PMCID:
PMC4700857
See all PubMed Citations (7)

Details of each submission

From Counsyl, SCV000678019.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000939965.3

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

Description

This sequence change creates a premature translational stop signal (p.Gln7Aspfs*14) in the ATP7B gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs749363958, ExAC 0.03%). This variant has been observed in an individual affected with Wilson disease (PMID: 15967699). ClinVar contains an entry for this variant (Variation ID: 419611). Loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). For these reasons, this variant has been classified as Pathogenic.

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

From Baylor Genetics, SCV001163740.1

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

From Nilou-Genome Lab, SCV001977202.1

#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 10, 2021

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