NM_000053.4(ATP7B):c.19_20del (p.Gln7fs) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(1);Uncertain significance(2) (Last evaluated: Feb 19, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000478984.6

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]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000567525GeneDxcriteria provided, single submitter
Uncertain significance
(Feb 19, 2021)
germlineclinical testing

Citation Link,

SCV000602607ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratoriescriteria provided, single submitter
Uncertain significance
(Nov 27, 2017)
germlineclinical testing

Citation Link,

SCV001149058CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Likely pathogenic
(Dec 1, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000567525.2

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

Description

Reported homozygous in a female pediatric patient with no symptoms of Wilson disease or abnormalities on liver biopsy (Stalke et al., 2019); Expression of mRNA in liver cells of a patient homozygous for the variant was in the range of healthy controls and in-vitro expression assays found mRNA and protein levels comparable to wild type, suggesting that the variant may bypass nonsense-mediated mRNA decay (NMD) allowing normal copper export (Stalke et al., 2019); This variant is associated with the following publications: (PMID: 18371106, 30291343, 26752957, 15967699, 30723317, 29649982, 31169307, 23486543, 31980526)

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000602607.2

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001149058.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 27, 2021

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