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NM_000053.4(ATP7B):c.2896del (p.Glu965_Val966insTer) AND Wilson disease

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 12, 2023
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:
RCV003503200.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.2896del (p.Glu965_Val966insTer)]

NM_000053.4(ATP7B):c.2896del (p.Glu965_Val966insTer)

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.2896del (p.Glu965_Val966insTer)
HGVS:
  • NC_000013.11:g.51946449del
  • NG_008806.1:g.70047del
  • NM_000053.4:c.2896delMANE SELECT
  • NM_001005918.3:c.2275del
  • NM_001243182.2:c.2563del
  • NM_001330578.2:c.2662del
  • NM_001330579.2:c.2644del
  • NM_001406511.1:c.2896del
  • NM_001406512.1:c.2896del
  • NM_001406513.1:c.2896del
  • NM_001406514.1:c.2863del
  • NM_001406515.1:c.2842del
  • NM_001406516.1:c.2842del
  • NM_001406517.1:c.2800del
  • NM_001406518.1:c.2800del
  • NM_001406519.1:c.2761del
  • NM_001406520.1:c.2752del
  • NM_001406521.1:c.2752del
  • NM_001406522.1:c.2752del
  • NM_001406523.1:c.2896del
  • NM_001406524.1:c.2719del
  • NM_001406525.1:c.2866-2157del
  • NM_001406526.1:c.2896del
  • NM_001406527.1:c.2662del
  • NM_001406528.1:c.2662del
  • NM_001406530.1:c.2656del
  • NM_001406531.1:c.2644del
  • NM_001406532.1:c.2644del
  • NM_001406534.1:c.2608del
  • NM_001406535.1:c.2731-2157del
  • NM_001406536.1:c.2566del
  • NM_001406537.1:c.2722-2157del
  • NM_001406538.1:c.2662del
  • NM_001406539.1:c.2467del
  • NM_001406540.1:c.2614-2157del
  • NM_001406541.1:c.2410del
  • NM_001406542.1:c.2410del
  • NM_001406543.1:c.2548del
  • NM_001406544.1:c.2314del
  • NM_001406545.1:c.2248del
  • NM_001406546.1:c.2380-2157del
  • NM_001406547.1:c.2218-2157del
  • NM_001406548.1:c.1606del
  • NP_000044.2:p.Glu965_Val966insTer
  • NP_001005918.1:p.Glu758_Val759insTer
  • NP_001230111.1:p.Glu854_Val855insTer
  • NP_001317507.1:p.Glu887_Val888insTer
  • NP_001317508.1:p.Glu881_Val882insTer
  • NP_001393440.1:p.Glu965_Val966insTer
  • NP_001393441.1:p.Glu965_Val966insTer
  • NP_001393442.1:p.Glu965_Val966insTer
  • NP_001393443.1:p.Glu954_Val955insTer
  • NP_001393444.1:p.Glu947_Val948insTer
  • NP_001393445.1:p.Glu947_Val948insTer
  • NP_001393446.1:p.Glu933_Val934insTer
  • NP_001393447.1:p.Glu933_Val934insTer
  • NP_001393448.1:p.Glu920_Val921insTer
  • NP_001393449.1:p.Glu917_Val918insTer
  • NP_001393450.1:p.Glu917_Val918insTer
  • NP_001393451.1:p.Glu917_Val918insTer
  • NP_001393452.1:p.Glu965_Val966insTer
  • NP_001393453.1:p.Glu906_Val907insTer
  • NP_001393455.1:p.Glu965_Val966insTer
  • NP_001393456.1:p.Glu887_Val888insTer
  • NP_001393457.1:p.Glu887_Val888insTer
  • NP_001393459.1:p.Glu885_Val886insTer
  • NP_001393460.1:p.Glu881_Val882insTer
  • NP_001393461.1:p.Glu881_Val882insTer
  • NP_001393463.1:p.Glu869_Val870insTer
  • NP_001393465.1:p.Glu855_Val856insTer
  • NP_001393467.1:p.Glu887_Val888insTer
  • NP_001393468.1:p.Glu822_Val823insTer
  • NP_001393470.1:p.Glu803_Val804insTer
  • NP_001393471.1:p.Glu803_Val804insTer
  • NP_001393472.1:p.Glu849_Val850insTer
  • NP_001393473.1:p.Glu771_Val772insTer
  • NP_001393474.1:p.Glu749_Val750insTer
  • NP_001393477.1:p.Glu535_Val536insTer
  • NC_000013.10:g.52520584del
  • NC_000013.10:g.52520585del
Molecular consequence:
  • NM_001406525.1:c.2866-2157del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406535.1:c.2731-2157del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406537.1:c.2722-2157del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406540.1:c.2614-2157del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406546.1:c.2380-2157del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406547.1:c.2218-2157del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000053.4:c.2896del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001005918.3:c.2275del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001243182.2:c.2563del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001330578.2:c.2662del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001330579.2:c.2644del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406511.1:c.2896del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406512.1:c.2896del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406513.1:c.2896del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406514.1:c.2863del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406515.1:c.2842del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406516.1:c.2842del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406517.1:c.2800del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406518.1:c.2800del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406519.1:c.2761del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406520.1:c.2752del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406521.1:c.2752del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406522.1:c.2752del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406523.1:c.2896del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406524.1:c.2719del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406526.1:c.2896del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406527.1:c.2662del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406528.1:c.2662del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406530.1:c.2656del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406531.1:c.2644del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406532.1:c.2644del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406534.1:c.2608del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406536.1:c.2566del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406538.1:c.2662del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406539.1:c.2467del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406541.1:c.2410del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406542.1:c.2410del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406543.1:c.2548del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406544.1:c.2314del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406545.1:c.2248del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406548.1:c.1606del - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004325733Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 12, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Null mutation of the murine ATP7B (Wilson disease) gene results in intracellular copper accumulation and late-onset hepatic nodular transformation.

Buiakova OI, Xu J, Lutsenko S, Zeitlin S, Das K, Das S, Ross BM, Mekios C, Scheinberg IH, Gilliam TC.

Hum Mol Genet. 1999 Sep;8(9):1665-71.

PubMed [citation]
PMID:
10441329

Frameshift and nonsense mutations in the gene for ATPase7B are associated with severe impairment of copper metabolism and with an early clinical manifestation of Wilson's disease.

Gromadzka G, Schmidt HH, Genschel J, Bochow B, Rodo M, Tarnacka B, Litwin T, Chabik G, Członkowska A.

Clin Genet. 2005 Dec;68(6):524-32.

PubMed [citation]
PMID:
16283883
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004325733.1

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

Description

This sequence change creates a premature translational stop signal (p.Val966*) in the ATP7B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with ATP7B-related conditions (PMID: 10453196). This variant is also known as 2662delG. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024