ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.4011del (p.Ile1338fs)
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.4011del (p.Ile1338fs)
Variation ID: 2026966 Accession: VCV002026966.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51937286 (GRCh38) [ NCBI UCSC ] 13: 52511422 (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 Nov 14, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.4011del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Ile1338fs frameshift NM_001005918.3:c.3390del NP_001005918.1:p.Ile1131fs frameshift NM_001243182.2:c.3678del NP_001230111.1:p.Ile1227fs frameshift NM_001330578.2:c.3777del NP_001317507.1:p.Ile1260fs frameshift NM_001330579.2:c.3759del NP_001317508.1:p.Ile1254fs frameshift NM_001406511.1:c.4009delC NP_001393440.1:p.Ile1338Leufs frameshift NM_001406512.1:c.4009delC NP_001393441.1:p.Ile1338Leufs frameshift NM_001406513.1:c.4003delC NP_001393442.1:p.Ile1336Leufs frameshift NM_001406514.1:c.3976delC NP_001393443.1:p.Ile1327Leufs frameshift NM_001406515.1:c.3955delC NP_001393444.1:p.Ile1320Leufs frameshift NM_001406516.1:c.3955delC NP_001393445.1:p.Ile1320Leufs frameshift NM_001406517.1:c.3913delC NP_001393446.1:p.Ile1306Leufs frameshift NM_001406518.1:c.3913delC NP_001393447.1:p.Ile1306Leufs frameshift NM_001406519.1:c.3874delC NP_001393448.1:p.Ile1293Leufs frameshift NM_001406520.1:c.3865delC NP_001393449.1:p.Ile1290Leufs frameshift NM_001406521.1:c.3865delC NP_001393450.1:p.Ile1290Leufs frameshift NM_001406522.1:c.3865delC NP_001393451.1:p.Ile1290Leufs frameshift NM_001406523.1:c.3826delC NP_001393452.1:p.Ile1277Leufs frameshift NM_001406524.1:c.3832delC NP_001393453.1:p.Ile1279Leufs frameshift NM_001406525.1:c.3814delC NP_001393454.1:p.Ile1273Leufs frameshift NM_001406526.1:c.3805delC NP_001393455.1:p.Ile1270Leufs frameshift NM_001406527.1:c.3775delC NP_001393456.1:p.Ile1260Leufs frameshift NM_001406528.1:c.3775delC NP_001393457.1:p.Ile1260Leufs frameshift NM_001406530.1:c.3769delC NP_001393459.1:p.Ile1258Leufs frameshift NM_001406531.1:c.3757delC NP_001393460.1:p.Ile1254Leufs frameshift NM_001406532.1:c.3757delC NP_001393461.1:p.Ile1254Leufs frameshift NM_001406534.1:c.3721delC NP_001393463.1:p.Ile1242Leufs frameshift NM_001406535.1:c.3679delC NP_001393464.1:p.Ile1228Leufs frameshift NM_001406536.1:c.3679delC NP_001393465.1:p.Ile1228Leufs frameshift NM_001406537.1:c.3670delC NP_001393466.1:p.Ile1225Leufs frameshift NM_001406538.1:c.3631delC NP_001393467.1:p.Ile1212Leufs frameshift NM_001406539.1:c.3580delC NP_001393468.1:p.Ile1195Leufs frameshift NM_001406540.1:c.3562delC NP_001393469.1:p.Ile1189Leufs frameshift NM_001406541.1:c.3523delC NP_001393470.1:p.Ile1176Leufs frameshift NM_001406542.1:c.3523delC NP_001393471.1:p.Ile1176Leufs frameshift NM_001406543.1:c.3517delC NP_001393472.1:p.Ile1174Leufs frameshift NM_001406544.1:c.3427delC NP_001393473.1:p.Ile1144Leufs frameshift NM_001406545.1:c.3361delC NP_001393474.1:p.Ile1122Leufs frameshift NM_001406546.1:c.3328delC NP_001393475.1:p.Ile1111Leufs frameshift NM_001406547.1:c.3166delC NP_001393476.1:p.Ile1057Leufs frameshift NM_001406548.1:c.2719delC NP_001393477.1:p.Ile908Leufs frameshift NC_000013.11:g.51937288del NC_000013.10:g.52511424del NG_008806.1:g.79209del - Protein change
- I1131fs, I1254fs, I1227fs, I1260fs, I1338fs
- Other names
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- Canonical SPDI
- NC_000013.11:51937285:GGG:GG
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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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Nov 14, 2022 | RCV002871629.2 |
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
(Nov 14, 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: SCV003233020.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant 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 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.Ile1338Leufs*55) in the ATP7B gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 128 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 |
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.