ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.4299del (p.Thr1434fs)
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.4299del (p.Thr1434fs)
Variation ID: 2166696 Accession: VCV002166696.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51934855 (GRCh38) [ NCBI UCSC ] 13: 52508991 (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 Oct 28, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.4299del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Thr1434fs frameshift NM_001005918.3:c.3678del NP_001005918.1:p.Thr1227fs frameshift NM_001243182.2:c.3966del NP_001230111.1:p.Thr1323fs frameshift NM_001330578.2:c.4065del NP_001317507.1:p.Thr1356fs frameshift NM_001330579.2:c.4047del NP_001317508.1:p.Thr1350fs frameshift NM_001406511.1:c.4299delG NP_001393440.1:p.Thr1434Argfs frameshift NM_001406512.1:c.4299delG NP_001393441.1:p.Thr1434Argfs frameshift NM_001406513.1:c.4293delG NP_001393442.1:p.Thr1432Argfs frameshift NM_001406514.1:c.4266delG NP_001393443.1:p.Thr1423Argfs frameshift NM_001406515.1:c.4245delG NP_001393444.1:p.Thr1416Argfs frameshift NM_001406516.1:c.4245delG NP_001393445.1:p.Thr1416Argfs frameshift NM_001406517.1:c.4203delG NP_001393446.1:p.Thr1402Argfs frameshift NM_001406518.1:c.4203delG NP_001393447.1:p.Thr1402Argfs frameshift NM_001406519.1:c.4164delG NP_001393448.1:p.Thr1389Argfs frameshift NM_001406520.1:c.4155delG NP_001393449.1:p.Thr1386Argfs frameshift NM_001406521.1:c.4155delG NP_001393450.1:p.Thr1386Argfs frameshift NM_001406522.1:c.4155delG NP_001393451.1:p.Thr1386Argfs frameshift NM_001406523.1:c.4116delG NP_001393452.1:p.Thr1373Argfs frameshift NM_001406524.1:c.4122delG NP_001393453.1:p.Thr1375Argfs frameshift NM_001406525.1:c.4104delG NP_001393454.1:p.Thr1369Argfs frameshift NM_001406526.1:c.4095delG NP_001393455.1:p.Thr1366Argfs frameshift NM_001406527.1:c.4065delG NP_001393456.1:p.Thr1356Argfs frameshift NM_001406528.1:c.4065delG NP_001393457.1:p.Thr1356Argfs frameshift NM_001406530.1:c.4059delG NP_001393459.1:p.Thr1354Argfs frameshift NM_001406531.1:c.4047delG NP_001393460.1:p.Thr1350Argfs frameshift NM_001406532.1:c.4047delG NP_001393461.1:p.Thr1350Argfs frameshift NM_001406534.1:c.4011delG NP_001393463.1:p.Thr1338Argfs frameshift NM_001406535.1:c.3969delG NP_001393464.1:p.Thr1324Argfs frameshift NM_001406536.1:c.3969delG NP_001393465.1:p.Thr1324Argfs frameshift NM_001406537.1:c.3960delG NP_001393466.1:p.Thr1321Argfs frameshift NM_001406538.1:c.3921delG NP_001393467.1:p.Thr1308Argfs frameshift NM_001406539.1:c.3870delG NP_001393468.1:p.Thr1291Argfs frameshift NM_001406540.1:c.3852delG NP_001393469.1:p.Thr1285Argfs frameshift NM_001406541.1:c.3813delG NP_001393470.1:p.Thr1272Argfs frameshift NM_001406542.1:c.3813delG NP_001393471.1:p.Thr1272Argfs frameshift NM_001406543.1:c.3807delG NP_001393472.1:p.Thr1270Argfs frameshift NM_001406544.1:c.3717delG NP_001393473.1:p.Thr1240Argfs frameshift NM_001406545.1:c.3651delG NP_001393474.1:p.Thr1218Argfs frameshift NM_001406546.1:c.3618delG NP_001393475.1:p.Thr1207Argfs frameshift NM_001406547.1:c.3456delG NP_001393476.1:p.Thr1153Argfs frameshift NM_001406548.1:c.3009delG NP_001393477.1:p.Thr1004Argfs frameshift NC_000013.11:g.51934855del NC_000013.10:g.52508991del NG_008806.1:g.81640del - Protein change
- T1323fs, T1356fs, T1350fs, T1434fs, T1227fs
- Other names
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- Canonical SPDI
- NC_000013.11:51934854:C:
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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 |
2578 | 2719 |
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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Oct 28, 2022 | RCV003091894.2 |
Submissions - Germline
Classification
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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
(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: SCV003481092.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
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 … (more)
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.Thr1434Argfs*23) in the ATP7B gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 32 amino acid(s) of the ATP7B protein. 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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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 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.