ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.4354_4357dup (p.Ser1453fs)
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
-
NM_000053.4(ATP7B):c.4354_4357dup (p.Ser1453fs)
Variation ID: 2161078 Accession: VCV002161078.2
- Type and length
-
Duplication, 4 bp
- Location
-
Cytogenetic: 13q14.3 13: 51934796-51934797 (GRCh38) [ NCBI UCSC ] 13: 52508932-52508933 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Jul 19, 2023 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000053.4:c.4354_4357dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Ser1453fs frameshift NM_001005918.3:c.3733_3736dup NP_001005918.1:p.Ser1246fs frameshift NM_001243182.2:c.4021_4024dup NP_001230111.1:p.Ser1342fs frameshift NM_001330578.2:c.4120_4123dup NP_001317507.1:p.Ser1375fs frameshift NM_001330579.2:c.4102_4105dup NP_001317508.1:p.Ser1369fs frameshift NM_001406511.1:c.4354_4357dup NP_001393440.1:p.Ser1453Leufs frameshift NM_001406512.1:c.4354_4357dup NP_001393441.1:p.Ser1453Leufs frameshift NM_001406513.1:c.4348_4351dup NP_001393442.1:p.Ser1451Leufs frameshift NM_001406514.1:c.4321_4324dup NP_001393443.1:p.Ser1442Leufs frameshift NM_001406515.1:c.4300_4303dup NP_001393444.1:p.Ser1435Leufs frameshift NM_001406516.1:c.4300_4303dup NP_001393445.1:p.Ser1435Leufs frameshift NM_001406517.1:c.4258_4261dup NP_001393446.1:p.Ser1421Leufs frameshift NM_001406518.1:c.4258_4261dup NP_001393447.1:p.Ser1421Leufs frameshift NM_001406519.1:c.4219_4222dup NP_001393448.1:p.Ser1408Leufs frameshift NM_001406520.1:c.4210_4213dup NP_001393449.1:p.Ser1405Leufs frameshift NM_001406521.1:c.4210_4213dup NP_001393450.1:p.Ser1405Leufs frameshift NM_001406522.1:c.4210_4213dup NP_001393451.1:p.Ser1405Leufs frameshift NM_001406523.1:c.4171_4174dup NP_001393452.1:p.Ser1392Leufs frameshift NM_001406524.1:c.4177_4180dup NP_001393453.1:p.Ser1394Leufs frameshift NM_001406525.1:c.4159_4162dup NP_001393454.1:p.Ser1388Leufs frameshift NM_001406526.1:c.4150_4153dup NP_001393455.1:p.Ser1385Leufs frameshift NM_001406527.1:c.4120_4123dup NP_001393456.1:p.Ser1375Leufs frameshift NM_001406528.1:c.4120_4123dup NP_001393457.1:p.Ser1375Leufs frameshift NM_001406530.1:c.4114_4117dup NP_001393459.1:p.Ser1373Leufs frameshift NM_001406531.1:c.4102_4105dup NP_001393460.1:p.Ser1369Leufs frameshift NM_001406532.1:c.4102_4105dup NP_001393461.1:p.Ser1369Leufs frameshift NM_001406534.1:c.4066_4069dup NP_001393463.1:p.Ser1357Leufs frameshift NM_001406535.1:c.4024_4027dup NP_001393464.1:p.Ser1343Leufs frameshift NM_001406536.1:c.4024_4027dup NP_001393465.1:p.Ser1343Leufs frameshift NM_001406537.1:c.4015_4018dup NP_001393466.1:p.Ser1340Leufs frameshift NM_001406538.1:c.3976_3979dup NP_001393467.1:p.Ser1327Leufs frameshift NM_001406539.1:c.3925_3928dup NP_001393468.1:p.Ser1310Leufs frameshift NM_001406540.1:c.3907_3910dup NP_001393469.1:p.Ser1304Leufs frameshift NM_001406541.1:c.3868_3871dup NP_001393470.1:p.Ser1291Leufs frameshift NM_001406542.1:c.3868_3871dup NP_001393471.1:p.Ser1291Leufs frameshift NM_001406543.1:c.3862_3865dup NP_001393472.1:p.Ser1289Leufs frameshift NM_001406544.1:c.3772_3775dup NP_001393473.1:p.Ser1259Leufs frameshift NM_001406545.1:c.3706_3709dup NP_001393474.1:p.Ser1237Leufs frameshift NM_001406546.1:c.3673_3676dup NP_001393475.1:p.Ser1226Leufs frameshift NM_001406547.1:c.3511_3514dup NP_001393476.1:p.Ser1172Leufs frameshift NM_001406548.1:c.3064_3067dup NP_001393477.1:p.Ser1023Leufs frameshift NC_000013.11:g.51934797_51934800dup NC_000013.10:g.52508933_52508936dup NG_008806.1:g.81695_81698dup - Protein change
- S1342fs, S1369fs, S1246fs, S1375fs, S1453fs
- Other names
- -
- Canonical SPDI
- NC_000013.11:51934796:ACCA:ACCAACCA
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
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.
-
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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. |
|||
ATP7B | - | - |
GRCh38 GRCh37 |
2850 | 2991 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (1) |
criteria provided, single submitter
|
Jul 19, 2023 | RCV003087864.2 |
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
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. |
|
---|---|---|---|---|---|
Pathogenic
(Jul 19, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Wilson disease
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV003474587.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
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 … (more)
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. ClinVar contains an entry for this variant (Variation ID: 2161078). 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.Ser1453Leufs*10) in the ATP7B gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 13 amino acid(s) of the ATP7B protein. For these reasons, this variant has been classified as Pathogenic. (less)
|
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 |
---|---|---|---|---|
ATP7B Gene Mutations in Croatian Patients with Wilson Disease. | Ljubić H | Genetic testing and molecular biomarkers | 2016 | PMID: 26799313 |
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.