ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.4093dup (p.Ser1365fs)
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.4093dup (p.Ser1365fs)
Variation ID: 2137508 Accession: VCV002137508.2
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51935623-51935624 (GRCh38) [ NCBI UCSC ] 13: 52509759-52509760 (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 14, 2024 Jul 26, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.4093dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Ser1365fs frameshift NM_001005918.3:c.3472dup NP_001005918.1:p.Ser1158fs frameshift NM_001243182.2:c.3760dup NP_001230111.1:p.Ser1254fs frameshift NM_001330578.2:c.3859dup NP_001317507.1:p.Ser1287fs frameshift NM_001330579.2:c.3841dup NP_001317508.1:p.Ser1281fs frameshift NM_001406511.1:c.4093dup NP_001393440.1:p.Ser1365Phefs frameshift NM_001406512.1:c.4093dup NP_001393441.1:p.Ser1365Phefs frameshift NM_001406513.1:c.4087dup NP_001393442.1:p.Ser1363Phefs frameshift NM_001406514.1:c.4060dup NP_001393443.1:p.Ser1354Phefs frameshift NM_001406515.1:c.4039dup NP_001393444.1:p.Ser1347Phefs frameshift NM_001406516.1:c.4039dup NP_001393445.1:p.Ser1347Phefs frameshift NM_001406517.1:c.3997dup NP_001393446.1:p.Ser1333Phefs frameshift NM_001406518.1:c.3997dup NP_001393447.1:p.Ser1333Phefs frameshift NM_001406519.1:c.3958dup NP_001393448.1:p.Ser1320Phefs frameshift NM_001406520.1:c.3949dup NP_001393449.1:p.Ser1317Phefs frameshift NM_001406521.1:c.3949dup NP_001393450.1:p.Ser1317Phefs frameshift NM_001406522.1:c.3949dup NP_001393451.1:p.Ser1317Phefs frameshift NM_001406523.1:c.3910dup NP_001393452.1:p.Ser1304Phefs frameshift NM_001406524.1:c.3916dup NP_001393453.1:p.Ser1306Phefs frameshift NM_001406525.1:c.3898dup NP_001393454.1:p.Ser1300Phefs frameshift NM_001406526.1:c.3889dup NP_001393455.1:p.Ser1297Phefs frameshift NM_001406527.1:c.3859dup NP_001393456.1:p.Ser1287Phefs frameshift NM_001406528.1:c.3859dup NP_001393457.1:p.Ser1287Phefs frameshift NM_001406530.1:c.3853dup NP_001393459.1:p.Ser1285Phefs frameshift NM_001406531.1:c.3841dup NP_001393460.1:p.Ser1281Phefs frameshift NM_001406532.1:c.3841dup NP_001393461.1:p.Ser1281Phefs frameshift NM_001406534.1:c.3805dup NP_001393463.1:p.Ser1269Phefs frameshift NM_001406535.1:c.3763dup NP_001393464.1:p.Ser1255Phefs frameshift NM_001406536.1:c.3763dup NP_001393465.1:p.Ser1255Phefs frameshift NM_001406537.1:c.3754dup NP_001393466.1:p.Ser1252Phefs frameshift NM_001406538.1:c.3715dup NP_001393467.1:p.Ser1239Phefs frameshift NM_001406539.1:c.3664dup NP_001393468.1:p.Ser1222Phefs frameshift NM_001406540.1:c.3646dup NP_001393469.1:p.Ser1216Phefs frameshift NM_001406541.1:c.3607dup NP_001393470.1:p.Ser1203Phefs frameshift NM_001406542.1:c.3607dup NP_001393471.1:p.Ser1203Phefs frameshift NM_001406543.1:c.3601dup NP_001393472.1:p.Ser1201Phefs frameshift NM_001406544.1:c.3511dup NP_001393473.1:p.Ser1171Phefs frameshift NM_001406545.1:c.3445dup NP_001393474.1:p.Ser1149Phefs frameshift NM_001406546.1:c.3412dup NP_001393475.1:p.Ser1138Phefs frameshift NM_001406547.1:c.3250dup NP_001393476.1:p.Ser1084Phefs frameshift NM_001406548.1:c.2803dup NP_001393477.1:p.Ser935Phefs frameshift NC_000013.11:g.51935624dup NC_000013.10:g.52509760dup NG_008806.1:g.80871dup - Protein change
- S1254fs, S1365fs, S1281fs, S1158fs, S1287fs
- Other names
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- Canonical SPDI
- NC_000013.11:51935623:A:AA
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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 |
2572 | 2712 |
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
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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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Jul 26, 2022 | RCV003058418.2 |
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
(Jul 26, 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: SCV003442230.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
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 … (more)
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. This variant is also known as c.4093InsT. This premature translational stop signal has been observed in individual(s) with Wilson disease (PMID: 23982005). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser1365Phefs*13) in the ATP7B gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 101 amino acid(s) of the ATP7B protein. (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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ATP7B Gene Mutations in Croatian Patients with Wilson Disease. | Ljubić H | Genetic testing and molecular biomarkers | 2016 | PMID: 26799313 |
Wilson's disease in Southern Brazil: genotype-phenotype correlation and description of two novel mutations in ATP7B gene. | Bem RS | Arquivos de neuro-psiquiatria | 2013 | PMID: 23982005 |
Text-mined citations for this variant ...
HelpRecord last updated Feb 14, 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.