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:: RCV003503200.1

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004325733	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 12, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10441329, 16283883, 10453196, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004325733

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 12, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Invitae, SCV004325733.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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