NM_000053.3(ATP7B):c.2947_2950delTGCC(C983Pfs*38) is expected to be pathogenic in the context of Wilson disease. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in ATP7B, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.
ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.2947_2950del (p.Cys983fs)
Germline
Classification
Help
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.
(1)
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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.
Likely pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000053.4(ATP7B):c.2947_2950del (p.Cys983fs)
Variation ID: 1724278 Accession: VCV001724278.2
- Type and length
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Microsatellite, 4 bp
- Location
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Cytogenetic: 13q14.3 13: 51946394-51946397 (GRCh38) [ NCBI UCSC ] 13: 52520530-52520533 (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 Nov 19, 2022 Dec 24, 2022 Feb 3, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000053.4:c.2947_2950del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Cys983fs frameshift NM_001005918.3:c.2326_2329del NP_001005918.1:p.Cys776fs frameshift NM_001243182.2:c.2614_2617del NP_001230111.1:p.Cys872fs frameshift NM_001330578.2:c.2713_2716del NP_001317507.1:p.Cys905fs frameshift NM_001330579.2:c.2695_2698del NP_001317508.1:p.Cys899fs frameshift NM_001406511.1:c.2943_2946TGCC[1] NP_001393440.1:p.Cys983Profs frameshift NM_001406512.1:c.2943_2946TGCC[1] NP_001393441.1:p.Cys983Profs frameshift NM_001406513.1:c.2943_2946TGCC[1] NP_001393442.1:p.Cys983Profs frameshift NM_001406514.1:c.2910_2913TGCC[1] NP_001393443.1:p.Cys972Profs frameshift NM_001406515.1:c.2889_2892TGCC[1] NP_001393444.1:p.Cys965Profs frameshift NM_001406516.1:c.2889_2892TGCC[1] NP_001393445.1:p.Cys965Profs frameshift NM_001406517.1:c.2847_2850TGCC[1] NP_001393446.1:p.Cys951Profs frameshift NM_001406518.1:c.2847_2850TGCC[1] NP_001393447.1:p.Cys951Profs frameshift NM_001406519.1:c.2808_2811TGCC[1] NP_001393448.1:p.Cys938Profs frameshift NM_001406520.1:c.2799_2802TGCC[1] NP_001393449.1:p.Cys935Profs frameshift NM_001406521.1:c.2799_2802TGCC[1] NP_001393450.1:p.Cys935Profs frameshift NM_001406522.1:c.2799_2802TGCC[1] NP_001393451.1:p.Cys935Profs frameshift NM_001406523.1:c.2943_2946TGCC[1] NP_001393452.1:p.Cys983Profs frameshift NM_001406524.1:c.2766_2769TGCC[1] NP_001393453.1:p.Cys924Profs frameshift NM_001406526.1:c.2943_2946TGCC[1] NP_001393455.1:p.Cys983Profs frameshift NM_001406527.1:c.2709_2712TGCC[1] NP_001393456.1:p.Cys905Profs frameshift NM_001406528.1:c.2709_2712TGCC[1] NP_001393457.1:p.Cys905Profs frameshift NM_001406530.1:c.2703_2706TGCC[1] NP_001393459.1:p.Cys903Profs frameshift NM_001406531.1:c.2691_2694TGCC[1] NP_001393460.1:p.Cys899Profs frameshift NM_001406532.1:c.2691_2694TGCC[1] NP_001393461.1:p.Cys899Profs frameshift NM_001406534.1:c.2655_2658TGCC[1] NP_001393463.1:p.Cys887Profs frameshift NM_001406536.1:c.2613_2616TGCC[1] NP_001393465.1:p.Cys873Profs frameshift NM_001406538.1:c.2709_2712TGCC[1] NP_001393467.1:p.Cys905Profs frameshift NM_001406539.1:c.2514_2517TGCC[1] NP_001393468.1:p.Cys840Profs frameshift NM_001406541.1:c.2457_2460TGCC[1] NP_001393470.1:p.Cys821Profs frameshift NM_001406542.1:c.2457_2460TGCC[1] NP_001393471.1:p.Cys821Profs frameshift NM_001406543.1:c.2595_2598TGCC[1] NP_001393472.1:p.Cys867Profs frameshift NM_001406544.1:c.2361_2364TGCC[1] NP_001393473.1:p.Cys789Profs frameshift NM_001406545.1:c.2295_2298TGCC[1] NP_001393474.1:p.Cys767Profs frameshift NM_001406548.1:c.1653_1656TGCC[1] NP_001393477.1:p.Cys553Profs frameshift NC_000013.11:g.51946394GGCA[1] NC_000013.10:g.52520530GGCA[1] NG_008806.1:g.70094TGCC[1] - Protein change
- C776fs, C872fs, C899fs, C905fs, C983fs
- Other names
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- Canonical SPDI
- NC_000013.11:51946393:GGCAGGCA:GGCA
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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
Help
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 | ||
|---|---|---|---|---|---|---|
| HI score
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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. |
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| ATP7B | - | - |
GRCh38 GRCh37 |
2918 | 3062 | |
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
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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. |
|---|---|---|---|---|
| Likely pathogenic (1) |
criteria provided, single submitter
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Feb 3, 2022 | RCV002309546.2 |
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
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. |
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Likely pathogenic
(Feb 03, 2022)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV002603423.2
First in ClinVar: Nov 19, 2022 Last updated: Dec 24, 2022 |
Comment:
NM_000053.3(ATP7B):c.2947_2950delTGCC(C983Pfs*38) is expected to be pathogenic in the context of Wilson disease. This variant is predicted to lead to an abnormal or absent protein product … (more)
NM_000053.3(ATP7B):c.2947_2950delTGCC(C983Pfs*38) is expected to be pathogenic in the context of Wilson disease. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in ATP7B, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening. (less)
|
Comment:
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. |
Comment:
NM_000053.3(ATP7B):c.2947_2950delTGCC(C983Pfs*38) is expected to be pathogenic in the context of Wilson disease. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in ATP7B, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Dec 24, 2022
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.