ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.4152dup (p.Glu1385Ter)
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.4152dup (p.Glu1385Ter)
Variation ID: 2020602 Accession: VCV002020602.3
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51935001-51935002 (GRCh38) [ NCBI UCSC ] 13: 52509137-52509138 (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 29, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.4152dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Glu1385Ter nonsense NM_000053.3:c.4152dup NM_001005918.3:c.3531dup NP_001005918.1:p.Glu1178Ter nonsense NM_001243182.2:c.3819dup NP_001230111.1:p.Glu1274Ter nonsense NM_001330578.2:c.3918dup NP_001317507.1:p.Glu1307Ter nonsense NM_001330579.2:c.3900dup NP_001317508.1:p.Glu1301Ter nonsense NM_001406511.1:c.4152dup NP_001393440.1:p.Glu1385Terfs frameshift nonsense NM_001406512.1:c.4152dup NP_001393441.1:p.Glu1385Terfs frameshift nonsense NM_001406513.1:c.4146dup NP_001393442.1:p.Glu1383Terfs frameshift nonsense NM_001406514.1:c.4119dup NP_001393443.1:p.Glu1374Terfs frameshift nonsense NM_001406515.1:c.4098dup NP_001393444.1:p.Glu1367Terfs frameshift nonsense NM_001406516.1:c.4098dup NP_001393445.1:p.Glu1367Terfs frameshift nonsense NM_001406517.1:c.4056dup NP_001393446.1:p.Glu1353Terfs frameshift nonsense NM_001406518.1:c.4056dup NP_001393447.1:p.Glu1353Terfs frameshift nonsense NM_001406519.1:c.4017dup NP_001393448.1:p.Glu1340Terfs frameshift nonsense NM_001406520.1:c.4008dup NP_001393449.1:p.Glu1337Terfs frameshift nonsense NM_001406521.1:c.4008dup NP_001393450.1:p.Glu1337Terfs frameshift nonsense NM_001406522.1:c.4008dup NP_001393451.1:p.Glu1337Terfs frameshift nonsense NM_001406523.1:c.3969dup NP_001393452.1:p.Glu1324Terfs frameshift nonsense NM_001406524.1:c.3975dup NP_001393453.1:p.Glu1326Terfs frameshift nonsense NM_001406525.1:c.3957dup NP_001393454.1:p.Glu1320Terfs frameshift nonsense NM_001406526.1:c.3948dup NP_001393455.1:p.Glu1317Terfs frameshift nonsense NM_001406527.1:c.3918dup NP_001393456.1:p.Glu1307Terfs frameshift nonsense NM_001406528.1:c.3918dup NP_001393457.1:p.Glu1307Terfs frameshift nonsense NM_001406530.1:c.3912dup NP_001393459.1:p.Glu1305Terfs frameshift nonsense NM_001406531.1:c.3900dup NP_001393460.1:p.Glu1301Terfs frameshift nonsense NM_001406532.1:c.3900dup NP_001393461.1:p.Glu1301Terfs frameshift nonsense NM_001406534.1:c.3864dup NP_001393463.1:p.Glu1289Terfs frameshift nonsense NM_001406535.1:c.3822dup NP_001393464.1:p.Glu1275Terfs frameshift nonsense NM_001406536.1:c.3822dup NP_001393465.1:p.Glu1275Terfs frameshift nonsense NM_001406537.1:c.3813dup NP_001393466.1:p.Glu1272Terfs frameshift nonsense NM_001406538.1:c.3774dup NP_001393467.1:p.Glu1259Terfs frameshift nonsense NM_001406539.1:c.3723dup NP_001393468.1:p.Glu1242Terfs frameshift nonsense NM_001406540.1:c.3705dup NP_001393469.1:p.Glu1236Terfs frameshift nonsense NM_001406541.1:c.3666dup NP_001393470.1:p.Glu1223Terfs frameshift nonsense NM_001406542.1:c.3666dup NP_001393471.1:p.Glu1223Terfs frameshift nonsense NM_001406543.1:c.3660dup NP_001393472.1:p.Glu1221Terfs frameshift nonsense NM_001406544.1:c.3570dup NP_001393473.1:p.Glu1191Terfs frameshift nonsense NM_001406545.1:c.3504dup NP_001393474.1:p.Glu1169Terfs frameshift nonsense NM_001406546.1:c.3471dup NP_001393475.1:p.Glu1158Terfs frameshift nonsense NM_001406547.1:c.3309dup NP_001393476.1:p.Glu1104Terfs frameshift nonsense NM_001406548.1:c.2862dup NP_001393477.1:p.Glu955Terfs frameshift nonsense NC_000013.11:g.51935002dup NC_000013.10:g.52509138dup NG_008806.1:g.81493dup - Protein change
- E1301*, E1274*, E1307*, E1385*, E1178*
- Other names
- p.Glu1385*
- Canonical SPDI
- NC_000013.11:51935001: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
Help
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
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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Jul 30, 2022 | RCV002857403.2 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Dec 29, 2022 | RCV003481338.1 |
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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Likely pathogenic
(Dec 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not provided
Affected status: unknown
Allele origin:
germline
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV004226636.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
PM2, PVS1
Number of individuals with the variant: 1
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Pathogenic
(Jul 30, 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: SCV003226162.2
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: 17949296, 26799313). This suggests … (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: 17949296, 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. 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.Glu1385*) in the ATP7B gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 81 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
HelpText-mined citations for this variant ...
HelpRecord last updated Feb 20, 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.