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NM_000053.4(ATP7B):c.3426G>C (p.Gln1142His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Oct 12, 2021)
Last evaluated:
Aug 10, 2021
Accession:
VCV000370151.5
Variation ID:
370151
Description:
single nucleotide variant
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NM_000053.4(ATP7B):c.3426G>C (p.Gln1142His)

Allele ID
358219
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q14.3
Genomic location
13: 51941211 (GRCh38) GRCh38 UCSC
13: 52515347 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.52515347C>G
NC_000013.11:g.51941211C>G
NG_008806.1:g.75284G>C
... more HGVS
Protein change
Q1142H, Q935H, Q1058H, Q1064H, Q1031H
Other names
-
Canonical SPDI
NC_000013.11:51941210:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA6988685
dbSNP: rs778749563
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Aug 10, 2021 RCV000409630.5
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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
1325 1389

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Dec 02, 2015)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: unknown
Counsyl
Accession: SCV000485394.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (9)
Uncertain significance
(Mar 08, 2020)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Invitae
Accession: SCV000934021.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces glutamine with histidine at codon 1142 of the ATP7B protein (p.Gln1142His). The glutamine residue is weakly conserved and there is a … (more)
Uncertain significance
(Aug 10, 2021)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001977554.1
Submitted: (Oct 12, 2021)
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
Targeted next-generation sequencing of the ATP7B gene for molecular diagnosis of Wilson disease. Poon KS Clinical biochemistry 2016 PMID: 26483271
Mutational characterization of ATP7B gene in 103 Wilson's disease patients from Southern China: identification of three novel mutations. Wei Z Neuroreport 2014 PMID: 25089800
In silico investigation of the ATP7B gene: insights from functional prediction of non-synonymous substitution to protein structure. Squitti R Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 2014 PMID: 24253677
A genetic study of Wilson's disease in the United Kingdom. Coffey AJ Brain : a journal of neurology 2013 PMID: 23518715
A structural model of the copper ATPase ATP7B to facilitate analysis of Wilson disease-causing mutations and studies of the transport mechanism. Schushan M Metallomics : integrated biometal science 2012 PMID: 22692182
Mutation analysis of 73 southern Chinese Wilson's disease patients: identification of 10 novel mutations and its clinical correlation. Wang LH Journal of human genetics 2011 PMID: 21796144
Mutational analysis of 65 Wilson disease patients in Hong Kong Chinese: identification of 17 novel mutations and its genetic heterogeneity. Mak CM Journal of human genetics 2008 PMID: 18034201
Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease. Wu ZY Archives of neurology 2001 PMID: 11405812
Molecular analysis of Wilson disease in Taiwan: identification of one novel mutation and evidence of haplotype-mutation association. Lee CC Journal of human genetics 2000 PMID: 11043508
Mutation analysis of Wilson disease in Taiwan and description of six new mutations. Tsai CH Human mutation 1998 PMID: 9829905

Text-mined citations for rs778749563...

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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 Nov 27, 2021