NM_000053.4(ATP7B):c.1745_1746del (p.Ile582fs) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 25, 2017
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:: RCV002399599.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.1745_1746del (p.Ile582fs)]

NM_000053.4(ATP7B):c.1745_1746del (p.Ile582fs)

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.1745_1746del (p.Ile582fs)

HGVS:

NC_000013.11:g.51964996_51964997del
NG_008806.1:g.51499_51500del
NM_000053.4:c.1745_1746delMANE SELECT
NM_001005918.3:c.1745_1746del
NM_001243182.2:c.1412_1413del
NM_001330578.2:c.1745_1746del
NM_001330579.2:c.1745_1746del
NP_000044.2:p.Ile582fs
NP_001005918.1:p.Ile582fs
NP_001230111.1:p.Ile471fs
NP_001317507.1:p.Ile582fs
NP_001317508.1:p.Ile582fs
NC_000013.10:g.52539131_52539132del
NC_000013.10:g.52539132_52539133del
NC_000013.11:g.51964995_51964996delTA
NM_000053.3:c.1745_1746del
NM_000053.3:c.1745_1746delTA
NM_000053.4:c.1745_1746delTAMANE SELECT
p.Ile582Argfs*25

Protein change:

I471fs

Links:

dbSNP: rs753962912

NCBI 1000 Genomes Browser:

rs753962912

Molecular consequence:

NM_000053.4:c.1745_1746del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001005918.3:c.1745_1746del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243182.2:c.1412_1413del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330578.2:c.1745_1746del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330579.2:c.1745_1746del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002711589	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Jan 25, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17317524, 23518715, 27398169 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002711589

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Jan 25, 2017)

germline

clinical testing

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

Citation Link

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

Late neurological presentations of Wilson disease patients in French population and identification of 8 novel mutations in the ATP7B gene.

Chappuis P, Callebert J, Quignon V, Woimant F, Laplanche JL.

J Trace Elem Med Biol. 2007;21(1):37-42. Epub 2007 Jan 16.

PubMed [citation]

PMID:: 17317524

A genetic study of Wilson's disease in the United Kingdom.

Coffey AJ, Durkie M, Hague S, McLay K, Emmerson J, Lo C, Klaffke S, Joyce CJ, Dhawan A, Hadzic N, Mieli-Vergani G, Kirk R, Elizabeth Allen K, Nicholl D, Wong S, Griffiths W, Smithson S, Giffin N, Taha A, Connolly S, Gillett GT, Tanner S, et al.

Brain. 2013 May;136(Pt 5):1476-87. doi: 10.1093/brain/awt035. Epub 2013 Mar 21.

PubMed [citation]

PMID:: 23518715
PMCID:: PMC3634195

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV002711589.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The c.1745_1746delTA pathogenic mutation, located in coding exon 5 of the ATP7B gene, results from a deletion of two nucleotides at nucleotide positions 1745 to 1746, causing a translational frameshift with a predicted alternate stop codon (p.I582Rfs*25). This mutation has been detected in multiple individuals with Wilson disease (Chappuis P et al. J Trace Elem Med Biol, 2007 Jan;21:37-42; Coffey AJ et al. Brain, 2013 May;136:1476-87; Hua R et al. Am J Transl Res, 2016 Jun;8:2851-61). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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: Sep 29, 2024

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