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NM_000053.4(ATP7B):c.3121C>T (p.Arg1041Trp)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Oct 12, 2021)
Last evaluated:
Aug 10, 2021
Accession:
VCV000312384.8
Variation ID:
312384
Description:
single nucleotide variant
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NM_000053.4(ATP7B):c.3121C>T (p.Arg1041Trp)

Allele ID
319974
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q14.3
Genomic location
13: 51944231 (GRCh38) GRCh38 UCSC
13: 52518367 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.11:g.51944231G>A
NG_008806.1:g.72264C>T
NM_000053.4:c.3121C>T MANE Select NP_000044.2:p.Arg1041Trp missense
... more HGVS
Protein change
R1041W, R834W, R930W, R957W, R963W
Other names
-
Canonical SPDI
NC_000013.11:51944230:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA6988802
UniProtKB: P35670#VAR_000754
dbSNP: rs746485916
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts Aug 10, 2021 RCV000308454.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATP7B - - GRCh38
GRCh37
1321 1385

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 24, 2020)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Invitae
Accession: SCV000752254.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (12)
Comment:
This sequence change replaces arginine with tryptophan at codon 1041 of the ATP7B protein (p.Arg1041Trp). The arginine residue is highly conserved and there is a … (more)
Likely pathogenic
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000384660.3
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (8)
Comment:
Across a selection of the available literature, the ATP7B c.3121C>T (p.Arg1041Trp) missense variant has been identified in a compound heterozygous state in four patients with … (more)
Likely pathogenic
(Aug 10, 2021)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001977275.1
Submitted: (Oct 12, 2021)
Evidence details
Likely pathogenic
(Mar 30, 2017)
no assertion criteria provided
Method: clinical testing
Wilson disease
Allele origin: unknown
Counsyl
Accession: SCV000790626.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (14)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Wilson disease
Allele origin: germline
Natera, Inc.
Accession: SCV001455595.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Spectrum and Classification of ATP7B Variants in a Large Cohort of Chinese Patients with Wilson's Disease Guides Genetic Diagnosis. Dong Y Theranostics 2016 PMID: 27022412
Spectrum of mutations in the ATP binding domain of ATP7B gene of Wilson Disease in a regional Indian cohort. Guggilla SR Gene 2015 PMID: 25982861
A genetic study of Wilson's disease in the United Kingdom. Coffey AJ Brain : a journal of neurology 2013 PMID: 23518715
Mutation analysis of ATP7B gene in Turkish Wilson disease patients: identification of five novel mutations. Simsek Papur O European journal of medical genetics 2013 PMID: 23333878
Molecular analysis of Wilson patients: direct sequencing and MLPA analysis in the ATP7B gene and Atox1 and COMMD1 gene analysis. Bost M Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS) 2012 PMID: 22677543
Clinical presentation and mutations in Danish patients with Wilson disease. Møller LB European journal of human genetics : EJHG 2011 PMID: 21610751
Mutation analysis and characterization of alternative splice variants of the Wilson disease gene ATP7B. Wan L Hepatology (Baltimore, Md.) 2010 PMID: 20931554
Genetic analysis of BIRC4/XIAP as a putative modifier gene of Wilson disease. Weiss KH Journal of inherited metabolic disease 2010 PMID: 20517649
High frequency of the c.3207C>A (p.H1069Q) mutation in ATP7B gene of Lithuanian patients with hepatic presentation of Wilson's disease. Kucinskas L World journal of gastroenterology 2008 PMID: 18855987
Sequence variation in the ATP-binding domain of the Wilson disease transporter, ATP7B, affects copper transport in a yeast model system. Hsi G Human mutation 2008 PMID: 18203200
Mutation analysis of the ATP7B gene and genotype/phenotype correlation in 227 patients with Wilson disease. Vrabelova S Molecular genetics and metabolism 2005 PMID: 15967699
Analysis of the human homologue of the canine copper toxicosis gene MURR1 in Wilson disease patients. Stuehler B Journal of molecular medicine (Berlin, Germany) 2004 PMID: 15205742
Wilson disease: novel mutations in the ATP7B gene and clinical correlation in Brazilian patients. Deguti MM Human mutation 2004 PMID: 15024742
Mutation analysis in patients of Mediterranean descent with Wilson disease: identification of 19 novel mutations. Loudianos G Journal of medical genetics 1999 PMID: 10544227
[Missense mutations of exons 14 and 18 of Wilson's disease gene in Chinese patients]. Wu Z Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 1999 PMID: 10194254
Further delineation of the molecular pathology of Wilson disease in the Mediterranean population. Loudianos G Human mutation 1998 PMID: 9671269

Text-mined citations for rs746485916...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021