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NM_000053.4(ATP7B):c.3556+1G>A

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Oct 12, 2021)
Last evaluated:
Aug 10, 2021
Accession:
VCV000189055.7
Variation ID:
189055
Description:
single nucleotide variant
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NM_000053.4(ATP7B):c.3556+1G>A

Allele ID
186880
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q14.3
Genomic location
13: 51941080 (GRCh38) GRCh38 UCSC
13: 52515216 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.52515216C>T
NC_000013.11:g.51941080C>T
NG_008806.1:g.75415G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000013.11:51941079:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
1000 Genomes Project 0.00020
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA274325
dbSNP: rs184388696
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 4 criteria provided, multiple submitters, no conflicts Aug 10, 2021 RCV000169452.7
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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
(Nov 11, 2014)
criteria provided, single submitter
Method: literature only
Wilson's disease
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220873.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Apr 01, 2019)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694449.2
Submitted: (Sep 24, 2019)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: ATP7B c.3556+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Pathogenic
(Oct 30, 2020)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Invitae
Accession: SCV001236884.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change affects a donor splice site in intron 16 of the ATP7B gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Aug 10, 2021)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001977246.1
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
ATP7B Gene Mutations in Croatian Patients with Wilson Disease. Ljubić H Genetic testing and molecular biomarkers 2016 PMID: 26799313
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 Clinical genetics 2005 PMID: 16283883
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Null mutation of the murine ATP7B (Wilson disease) gene results in intracellular copper accumulation and late-onset hepatic nodular transformation. Buiakova OI Human molecular genetics 1999 PMID: 10441329
The Wilson disease gene: spectrum of mutations and their consequences. Thomas GR Nature genetics 1995 PMID: 7626145

Text-mined citations for rs184388696...

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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