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NM_000053.4(ATP7B):c.2687del (p.Leu896fs) AND Wilson disease

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 16, 2022
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:
RCV002308382.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.2687del (p.Leu896fs)]

NM_000053.4(ATP7B):c.2687del (p.Leu896fs)

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.2687del (p.Leu896fs)
HGVS:
  • NC_000013.11:g.51950052del
  • NG_008806.1:g.66445del
  • NM_000053.4:c.2687delMANE SELECT
  • NM_001005918.3:c.2201del
  • NM_001243182.2:c.2354del
  • NM_001330578.2:c.2453del
  • NM_001330579.2:c.2435del
  • NM_001406511.1:c.2685delT
  • NM_001406512.1:c.2685delT
  • NM_001406513.1:c.2685delT
  • NM_001406514.1:c.2652delT
  • NM_001406515.1:c.2685delT
  • NM_001406516.1:c.2685delT
  • NM_001406517.1:c.2589delT
  • NM_001406518.1:c.2589delT
  • NM_001406519.1:c.2685delT
  • NM_001406520.1:c.2541delT
  • NM_001406521.1:c.2541delT
  • NM_001406522.1:c.2541delT
  • NM_001406523.1:c.2685delT
  • NM_001406524.1:c.2508delT
  • NM_001406525.1:c.2685delT
  • NM_001406526.1:c.2685delT
  • NM_001406527.1:c.2451delT
  • NM_001406528.1:c.2451delT
  • NM_001406530.1:c.2445delT
  • NM_001406531.1:c.2433delT
  • NM_001406532.1:c.2433delT
  • NM_001406534.1:c.2451delT
  • NM_001406535.1:c.2685delT
  • NM_001406536.1:c.2355delT
  • NM_001406537.1:c.2541delT
  • NM_001406538.1:c.2451delT
  • NM_001406539.1:c.2256delT
  • NM_001406540.1:c.2433delT
  • NM_001406541.1:c.2199delT
  • NM_001406542.1:c.2199delT
  • NM_001406543.1:c.2337delT
  • NM_001406544.1:c.2103delT
  • NM_001406545.1:c.2037delT
  • NM_001406546.1:c.2199delT
  • NM_001406547.1:c.2037delT
  • NM_001406548.1:c.1395delT
  • NP_000044.2:p.Leu896fs
  • NP_001005918.1:p.Leu734fs
  • NP_001230111.1:p.Leu785fs
  • NP_001317507.1:p.Leu818fs
  • NP_001317508.1:p.Leu812fs
  • NP_001393440.1:p.Leu896Trpfs
  • NP_001393441.1:p.Leu896Trpfs
  • NP_001393442.1:p.Leu896Trpfs
  • NP_001393443.1:p.Leu885Trpfs
  • NP_001393444.1:p.Leu896Trpfs
  • NP_001393445.1:p.Leu896Trpfs
  • NP_001393446.1:p.Leu864Trpfs
  • NP_001393447.1:p.Leu864Trpfs
  • NP_001393448.1:p.Leu896Trpfs
  • NP_001393449.1:p.Leu848Trpfs
  • NP_001393450.1:p.Leu848Trpfs
  • NP_001393451.1:p.Leu848Trpfs
  • NP_001393452.1:p.Leu896Trpfs
  • NP_001393453.1:p.Leu837Trpfs
  • NP_001393454.1:p.Leu896Trpfs
  • NP_001393455.1:p.Leu896Trpfs
  • NP_001393456.1:p.Leu818Trpfs
  • NP_001393457.1:p.Leu818Trpfs
  • NP_001393459.1:p.Leu816Trpfs
  • NP_001393460.1:p.Leu812Trpfs
  • NP_001393461.1:p.Leu812Trpfs
  • NP_001393463.1:p.Leu818Trpfs
  • NP_001393464.1:p.Leu896Trpfs
  • NP_001393465.1:p.Leu786Trpfs
  • NP_001393466.1:p.Leu848Trpfs
  • NP_001393467.1:p.Leu818Trpfs
  • NP_001393468.1:p.Leu753Trpfs
  • NP_001393469.1:p.Leu812Trpfs
  • NP_001393470.1:p.Leu734Trpfs
  • NP_001393471.1:p.Leu734Trpfs
  • NP_001393472.1:p.Leu780Trpfs
  • NP_001393473.1:p.Leu702Trpfs
  • NP_001393474.1:p.Leu680Trpfs
  • NP_001393475.1:p.Leu734Trpfs
  • NP_001393476.1:p.Leu680Trpfs
  • NP_001393477.1:p.Leu466Trpfs
  • NC_000013.10:g.52524188del
Protein change:
L734fs
Molecular consequence:
  • NM_000053.4:c.2687del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001005918.3:c.2201del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001243182.2:c.2354del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330578.2:c.2453del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330579.2:c.2435del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406511.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406512.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406513.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406514.1:c.2652delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406515.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406516.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406517.1:c.2589delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406518.1:c.2589delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406519.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406520.1:c.2541delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406521.1:c.2541delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406522.1:c.2541delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406523.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406524.1:c.2508delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406525.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406526.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406527.1:c.2451delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406528.1:c.2451delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406530.1:c.2445delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406531.1:c.2433delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406532.1:c.2433delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406534.1:c.2451delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406535.1:c.2685delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406536.1:c.2355delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406537.1:c.2541delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406538.1:c.2451delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406539.1:c.2256delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406540.1:c.2433delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406541.1:c.2199delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406542.1:c.2199delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406543.1:c.2337delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406544.1:c.2103delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406545.1:c.2037delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406546.1:c.2199delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406547.1:c.2037delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406548.1:c.1395delT - 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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002602077Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))		Likely pathogenic
(Mar 16, 2022) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV002602077.2

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

Description

NM_000053.3(ATP7B):c.2687delT(L896Wfs*5) is expected to be pathogenic in the context of Wilson disease. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in ATP7B, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

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

Last Updated: Dec 24, 2022