ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.4229G>A (p.Trp1410Ter)
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.4229G>A (p.Trp1410Ter)
Variation ID: 1929153 Accession: VCV001929153.4
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51934925 (GRCh38) [ NCBI UCSC ] 13: 52509061 (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 7, 2023 Feb 28, 2024 Apr 7, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.4229G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Trp1410Ter nonsense NM_001005918.3:c.3608G>A NP_001005918.1:p.Trp1203Ter nonsense NM_001243182.2:c.3896G>A NP_001230111.1:p.Trp1299Ter nonsense NM_001330578.2:c.3995G>A NP_001317507.1:p.Trp1332Ter nonsense NM_001330579.2:c.3977G>A NP_001317508.1:p.Trp1326Ter nonsense NM_001406511.1:c.4229G>A NP_001393440.1:p.Trp1410Ter nonsense NM_001406512.1:c.4229G>A NP_001393441.1:p.Trp1410Ter nonsense NM_001406513.1:c.4223G>A NP_001393442.1:p.Trp1408Ter nonsense NM_001406514.1:c.4196G>A NP_001393443.1:p.Trp1399Ter nonsense NM_001406515.1:c.4175G>A NP_001393444.1:p.Trp1392Ter nonsense NM_001406516.1:c.4175G>A NP_001393445.1:p.Trp1392Ter nonsense NM_001406517.1:c.4133G>A NP_001393446.1:p.Trp1378Ter nonsense NM_001406518.1:c.4133G>A NP_001393447.1:p.Trp1378Ter nonsense NM_001406519.1:c.4094G>A NP_001393448.1:p.Trp1365Ter nonsense NM_001406520.1:c.4085G>A NP_001393449.1:p.Trp1362Ter nonsense NM_001406521.1:c.4085G>A NP_001393450.1:p.Trp1362Ter nonsense NM_001406522.1:c.4085G>A NP_001393451.1:p.Trp1362Ter nonsense NM_001406523.1:c.4046G>A NP_001393452.1:p.Trp1349Ter nonsense NM_001406524.1:c.4052G>A NP_001393453.1:p.Trp1351Ter nonsense NM_001406525.1:c.4034G>A NP_001393454.1:p.Trp1345Ter nonsense NM_001406526.1:c.4025G>A NP_001393455.1:p.Trp1342Ter nonsense NM_001406527.1:c.3995G>A NP_001393456.1:p.Trp1332Ter nonsense NM_001406528.1:c.3995G>A NP_001393457.1:p.Trp1332Ter nonsense NM_001406530.1:c.3989G>A NP_001393459.1:p.Trp1330Ter nonsense NM_001406531.1:c.3977G>A NP_001393460.1:p.Trp1326Ter nonsense NM_001406532.1:c.3977G>A NP_001393461.1:p.Trp1326Ter nonsense NM_001406534.1:c.3941G>A NP_001393463.1:p.Trp1314Ter nonsense NM_001406535.1:c.3899G>A NP_001393464.1:p.Trp1300Ter nonsense NM_001406536.1:c.3899G>A NP_001393465.1:p.Trp1300Ter nonsense NM_001406537.1:c.3890G>A NP_001393466.1:p.Trp1297Ter nonsense NM_001406538.1:c.3851G>A NP_001393467.1:p.Trp1284Ter nonsense NM_001406539.1:c.3800G>A NP_001393468.1:p.Trp1267Ter nonsense NM_001406540.1:c.3782G>A NP_001393469.1:p.Trp1261Ter nonsense NM_001406541.1:c.3743G>A NP_001393470.1:p.Trp1248Ter nonsense NM_001406542.1:c.3743G>A NP_001393471.1:p.Trp1248Ter nonsense NM_001406543.1:c.3737G>A NP_001393472.1:p.Trp1246Ter nonsense NM_001406544.1:c.3647G>A NP_001393473.1:p.Trp1216Ter nonsense NM_001406545.1:c.3581G>A NP_001393474.1:p.Trp1194Ter nonsense NM_001406546.1:c.3548G>A NP_001393475.1:p.Trp1183Ter nonsense NM_001406547.1:c.3386G>A NP_001393476.1:p.Trp1129Ter nonsense NM_001406548.1:c.2939G>A NP_001393477.1:p.Trp980Ter nonsense NC_000013.11:g.51934925C>T NC_000013.10:g.52509061C>T NG_008806.1:g.81570G>A - Protein change
- W1203*, W1284*, W1332*, W1378*, W1194*, W1216*, W1300*, W1326*, W1351*, W1410*, W980*, W1183*, W1246*, W1261*, W1267*, W1297*, W1299*, W1314*, W1330*, W1345*, W1392*, W1408*, W1129*, W1248*, W1342*, W1349*, W1362*, W1365*, W1399*
- Other names
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- Canonical SPDI
- NC_000013.11:51934924: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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- 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 |
2850 | 2991 |
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 (2) |
criteria provided, multiple submitters, no conflicts
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Apr 7, 2023 | RCV002618588.3 |
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
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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
(Oct 28, 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: SCV002968860.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 28, 2024 |
Comment:
This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp1410*) in the ATP7B gene. … (more)
This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp1410*) in the ATP7B gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 56 amino acid(s) of the ATP7B protein. This premature translational stop signal has been observed in individual(s) with Wilson disease (PMID: 18483695). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the ATP7B protein in which other variant(s) (p.Arg1459Glyfs*2) have been determined to be pathogenic (PMID: 26799313). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. (less)
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Likely pathogenic
(Apr 07, 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: SCV004216440.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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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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ATP7B Gene Mutations in Croatian Patients with Wilson Disease. | Ljubić H | Genetic testing and molecular biomarkers | 2016 | PMID: 26799313 |
Mutational analysis of ATP7B gene in Egyptian children with Wilson disease: 12 novel mutations. | Abdelghaffar TY | Journal of human genetics | 2008 | PMID: 18483695 |
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.