ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.3517G>A (p.Glu1173Lys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000053.4(ATP7B):c.3517G>A (p.Glu1173Lys)
Variation ID: 189050 Accession: VCV000189050.20
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51941120 (GRCh38) [ NCBI UCSC ] 13: 52515256 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Mar 29, 2015 Jun 17, 2024 Feb 5, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.3517G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Glu1173Lys missense NM_001005918.3:c.2896G>A NP_001005918.1:p.Glu966Lys missense NM_001243182.2:c.3184G>A NP_001230111.1:p.Glu1062Lys missense NM_001330578.2:c.3283G>A NP_001317507.1:p.Glu1095Lys missense NM_001330579.2:c.3265G>A NP_001317508.1:p.Glu1089Lys missense NC_000013.11:g.51941120C>T NC_000013.10:g.52515256C>T NG_008806.1:g.75375G>A P35670:p.Glu1173Lys - Protein change
- E1173K, E966K, E1062K, E1089K, E1095K
- Other names
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- Canonical SPDI
- NC_000013.11:51941119:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
The Genome Aggregation Database (gnomAD) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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ATP7B | - | - |
GRCh38 GRCh37 |
2926 | 3070 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (10) |
criteria provided, multiple submitters, no conflicts
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Feb 5, 2024 | RCV000169445.24 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Apr 13, 2017)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694448.1
First in ClinVar: Dec 26, 2017 Last updated: Dec 26, 2017 |
Comment:
Variant summary: The ATP7B c.3517G>A (p.Glu1173Lys) variant involves the alteration of a conserved nucleotide, resulting in a missense substitution. The variant lies within the HAD-like … (more)
Variant summary: The ATP7B c.3517G>A (p.Glu1173Lys) variant involves the alteration of a conserved nucleotide, resulting in a missense substitution. The variant lies within the HAD-like domain and P-type ATPase, cytoplasmic domain N (InterPro). 4/5 in silico tools predict a damaging outcome for this variant. This variant was found in the large control database ExAC and control cohorts in the literature at a frequency of 0.0000082 (1/121248 control chromosomes), which does not exceed the estimated maximal expected allele frequency of a pathogenic ATP7B variant (0.0054006). Multiple publications have reported the variant in Wilson disease patients. One study that provided familial genotyping data to confirm inheritance of the variant of interest along with a second pathogenic allele (Lee_TP7B_JHG_2000). One clinical diagnostic laboratory and several reputable databases have classified this variant as likely pathogenic or pathogenic. Taken together, this variant is classified as pathogenic. (less)
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Likely pathogenic
(Nov 06, 2014)
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criteria provided, single submitter
Method: literature only
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Wilson's disease
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000220864.2
First in ClinVar: Mar 29, 2015 Last updated: Dec 24, 2022 |
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Pathogenic
(Dec 22, 2023)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000626855.6
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1173 of the ATP7B protein … (more)
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1173 of the ATP7B protein (p.Glu1173Lys). This variant is present in population databases (rs756029120, gnomAD 0.01%). This missense change has been observed in individual(s) with Wilson disease (PMID: 10544227, 17680703, 23275100, 23843956, 27022412; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 189050). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ATP7B protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects ATP7B function (PMID: 20333758). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Aug 16, 2018)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000915633.1
First in ClinVar: May 27, 2019 Last updated: May 27, 2019 |
Comment:
The ATP7B c.3517G>A (p.Glu1173Lys) missense variant has been reported in seven studies in which it is found in a compound heterozygous state in at least … (more)
The ATP7B c.3517G>A (p.Glu1173Lys) missense variant has been reported in seven studies in which it is found in a compound heterozygous state in at least seven patients and in a heterozygous state in at least eight patients, all with Wilson disease (Loudianos et al. 1999; Lee et al. 2000; Chappuis et al. 2007; Geng et al. 2013; Gu et al. 2013; Cheng et al. 2014; Dong et al. 2016). In at least one family in which the patient was compound heterozygous for the p.Glu1173Lys variant and a missense variant, the unaffected sister and father were identified to be heterozygous for the p.Glu1173Lys variant while the unaffected mother was heterozygous for the other missense variant. This variant was absent from at least 77 controls and is reported at a frequency of 0.000012 in the total population from the Genome Aggregation Database. Based on the evidence, the p.Glu1173Lys variant is classified as pathogenic for Wilson disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
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Likely pathogenic
(Aug 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001977251.1
First in ClinVar: Oct 16, 2021 Last updated: Oct 16, 2021 |
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Pathogenic
(Jan 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002810891.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Mar 31, 2023)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV004238442.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
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Pathogenic
(Feb 05, 2024)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004845340.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
This missense variant replaces glutamic acid with lysine at codon 1173 of the ATP7B protein. Computational prediction suggests that this variant may have deleterious impact … (more)
This missense variant replaces glutamic acid with lysine at codon 1173 of the ATP7B protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). This variant alters a conserved glutamic acid residue in the N domain of the ATP7B protein (a.a. 1032 - 1196), a highly conserved region that is considered to be important for ATP7B protein function (PMID: 35245129; ClinVar). To our knowledge, functional studies have not been reported for this variant. This variant has been observed in individuals affected with autosomal recessive Wilson disease (PMID: 10544227, 11043508, 11405812, 11775208, 14986826, 17317524, 23275100, 23843956, 24718822, 27022412, 30702195), including in 1 individual in the homozygous state (PMID: 27022412) and in 10 individuals in the compound heterozygous state or in unknown phase with a second pathogenic variant in the ATP7B gene (PMID: 10544227, 11043508, 11775208, 17317524, 23275100, 23843956, 24718822, 30702195). This variant has been identified in 3/249590 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. (less)
Number of individuals with the variant: 3
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Pathogenic
(Nov 19, 2023)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004216335.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001455586.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Structure of the Wilson disease copper transporter ATP7B. | Bitter RM | Science advances | 2022 | PMID: 35245129 |
Complex ATP7B mutation patterns in Wilson disease and evaluation of a yeast model for functional analysis of variants. | Li X | Human mutation | 2019 | PMID: 30702195 |
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 |
Wilson disease in the South chinese han population. | Cheng N | The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques | 2014 | PMID: 24718822 |
Novel ATPase Cu(2+) transporting beta polypeptide mutations in Chinese families with Wilson's disease. | Gu S | PloS one | 2013 | PMID: 23843956 |
Identification of one novel and nine recurrent mutations of the ATP7B gene in 11 children with Wilson disease. | Geng J | World journal of pediatrics : WJP | 2013 | PMID: 23275100 |
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 |
Functional analysis of mutations in the ATP loop of the Wilson disease copper transporter, ATP7B. | Luoma LM | Human mutation | 2010 | PMID: 20333758 |
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 |
Sequence variation database for the Wilson disease copper transporter, ATP7B. | Kenney SM | Human mutation | 2007 | PMID: 17680703 |
Late neurological presentations of Wilson disease patients in French population and identification of 8 novel mutations in the ATP7B gene. | Chappuis P | Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS) | 2007 | PMID: 17317524 |
Mutation spectrum and polymorphisms in ATP7B identified on direct sequencing of all exons in Chinese Han and Hui ethnic patients with Wilson's disease. | Gu YH | Clinical genetics | 2003 | PMID: 14986826 |
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 |
Identification and analysis of mutations of the Wilson disease gene in Chinese population. | Wu Z | Chinese medical journal | 2000 | PMID: 11775208 |
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 in patients of Mediterranean descent with Wilson disease: identification of 19 novel mutations. | Loudianos G | Journal of medical genetics | 1999 | PMID: 10544227 |
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Text-mined citations for rs756029120 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.