ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.3727del (p.Val1243fs)
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.3727del (p.Val1243fs)
Variation ID: 2019035 Accession: VCV002019035.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51937652 (GRCh38) [ NCBI UCSC ] 13: 52511788 (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 Feb 8, 2023 Feb 20, 2024 Dec 23, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.3727del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Val1243fs frameshift NM_001005918.3:c.3106del NP_001005918.1:p.Val1036fs frameshift NM_001243182.2:c.3394del NP_001230111.1:p.Val1132fs frameshift NM_001330578.2:c.3493del NP_001317507.1:p.Val1165fs frameshift NM_001330579.2:c.3475del NP_001317508.1:p.Val1159fs frameshift NM_001406511.1:c.3726delG NP_001393440.1:p.Val1243Cysfs frameshift NM_001406512.1:c.3726delG NP_001393441.1:p.Val1243Cysfs frameshift NM_001406513.1:c.3720delG NP_001393442.1:p.Val1241Cysfs frameshift NM_001406514.1:c.3693delG NP_001393443.1:p.Val1232Cysfs frameshift NM_001406515.1:c.3672delG NP_001393444.1:p.Val1225Cysfs frameshift NM_001406516.1:c.3672delG NP_001393445.1:p.Val1225Cysfs frameshift NM_001406517.1:c.3630delG NP_001393446.1:p.Val1211Cysfs frameshift NM_001406518.1:c.3630delG NP_001393447.1:p.Val1211Cysfs frameshift NM_001406519.1:c.3591delG NP_001393448.1:p.Val1198Cysfs frameshift NM_001406520.1:c.3582delG NP_001393449.1:p.Val1195Cysfs frameshift NM_001406521.1:c.3582delG NP_001393450.1:p.Val1195Cysfs frameshift NM_001406522.1:c.3582delG NP_001393451.1:p.Val1195Cysfs frameshift NM_001406523.1:c.3543delG NP_001393452.1:p.Val1182Cysfs frameshift NM_001406524.1:c.3549delG NP_001393453.1:p.Val1184Cysfs frameshift NM_001406525.1:c.3531delG NP_001393454.1:p.Val1178Cysfs frameshift NM_001406527.1:c.3492delG NP_001393456.1:p.Val1165Cysfs frameshift NM_001406528.1:c.3492delG NP_001393457.1:p.Val1165Cysfs frameshift NM_001406530.1:c.3486delG NP_001393459.1:p.Val1163Cysfs frameshift NM_001406531.1:c.3474delG NP_001393460.1:p.Val1159Cysfs frameshift NM_001406532.1:c.3474delG NP_001393461.1:p.Val1159Cysfs frameshift NM_001406534.1:c.3438delG NP_001393463.1:p.Val1147Cysfs frameshift NM_001406535.1:c.3396delG NP_001393464.1:p.Val1133Cysfs frameshift NM_001406536.1:c.3396delG NP_001393465.1:p.Val1133Cysfs frameshift NM_001406537.1:c.3387delG NP_001393466.1:p.Val1130Cysfs frameshift NM_001406538.1:c.3348delG NP_001393467.1:p.Val1117Cysfs frameshift NM_001406539.1:c.3297delG NP_001393468.1:p.Val1100Cysfs frameshift NM_001406540.1:c.3279delG NP_001393469.1:p.Val1094Cysfs frameshift NM_001406541.1:c.3240delG NP_001393470.1:p.Val1081Cysfs frameshift NM_001406542.1:c.3240delG NP_001393471.1:p.Val1081Cysfs frameshift NM_001406543.1:c.3234delG NP_001393472.1:p.Val1079Cysfs frameshift NM_001406544.1:c.3144delG NP_001393473.1:p.Val1049Cysfs frameshift NM_001406545.1:c.3078delG NP_001393474.1:p.Val1027Cysfs frameshift NM_001406546.1:c.3045delG NP_001393475.1:p.Val1016Cysfs frameshift NM_001406547.1:c.2883delG NP_001393476.1:p.Val962Cysfs frameshift NM_001406548.1:c.2436delG NP_001393477.1:p.Val813Cysfs frameshift NC_000013.11:g.51937653del NC_000013.10:g.52511789del NG_008806.1:g.78843del - Protein change
- V1159fs, V1132fs, V1165fs, V1243fs, V1036fs
- Other names
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- Canonical SPDI
- NC_000013.11:51937651:CC:C
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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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- 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 |
2857 | 2999 |
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 (1) |
criteria provided, single submitter
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Dec 23, 2022 | RCV002870966.2 |
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
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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
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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
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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
(Dec 23, 2022)
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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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Invitae
Accession: SCV003222476.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ATP7B-related conditions. … (more)
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ATP7B-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Val1243Cysfs*87) in the ATP7B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). (less)
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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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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 |
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 |
Text-mined citations for this variant ...
HelpRecord last updated Feb 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.