This variant deletes 1 nucleotide in exon 2 of the ATP7B gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, this variant has not been reported in individuals affected with ATP7B-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of ATP7B function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.1161del (p.Gln388fs)
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.
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.1161del (p.Gln388fs)
Variation ID: 3075398 Accession: VCV003075398.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51974059 (GRCh38) [ NCBI UCSC ] 13: 52548195 (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 Apr 20, 2024 Apr 20, 2024 Feb 5, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000053.4:c.1161del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Gln388fs frameshift NM_001005918.3:c.1161del NP_001005918.1:p.Gln388fs frameshift NM_001243182.2:c.828del NP_001230111.1:p.Gln277fs frameshift NM_001330578.2:c.1161del NP_001317507.1:p.Gln388fs frameshift NM_001330579.2:c.1161del NP_001317508.1:p.Gln388fs frameshift NM_001406511.1:c.1161del NP_001393440.1:p.Gln388fs frameshift NM_001406512.1:c.1161del NP_001393441.1:p.Gln388fs frameshift NM_001406513.1:c.1161del NP_001393442.1:p.Gln388fs frameshift NM_001406514.1:c.1161del NP_001393443.1:p.Gln388fs frameshift NM_001406515.1:c.1161del NP_001393444.1:p.Gln388fs frameshift NM_001406516.1:c.1161del NP_001393445.1:p.Gln388fs frameshift NM_001406517.1:c.1065del NP_001393446.1:p.Gln356fs frameshift NM_001406518.1:c.1065del NP_001393447.1:p.Gln356fs frameshift NM_001406519.1:c.1161del NP_001393448.1:p.Gln388fs frameshift NM_001406520.1:c.1161del NP_001393449.1:p.Gln388fs frameshift NM_001406521.1:c.1161del NP_001393450.1:p.Gln388fs frameshift NM_001406522.1:c.1161del NP_001393451.1:p.Gln388fs frameshift NM_001406523.1:c.1161del NP_001393452.1:p.Gln388fs frameshift NM_001406524.1:c.1161del NP_001393453.1:p.Gln388fs frameshift NM_001406525.1:c.1161del NP_001393454.1:p.Gln388fs frameshift NM_001406526.1:c.1161del NP_001393455.1:p.Gln388fs frameshift NM_001406527.1:c.1161del NP_001393456.1:p.Gln388fs frameshift NM_001406528.1:c.1161del NP_001393457.1:p.Gln388fs frameshift NM_001406530.1:c.1065del NP_001393459.1:p.Gln356fs frameshift NM_001406531.1:c.1161del NP_001393460.1:p.Gln388fs frameshift NM_001406532.1:c.1161del NP_001393461.1:p.Gln388fs frameshift NM_001406534.1:c.1161del NP_001393463.1:p.Gln388fs frameshift NM_001406535.1:c.1161del NP_001393464.1:p.Gln388fs frameshift NM_001406536.1:c.1065del NP_001393465.1:p.Gln356fs frameshift NM_001406537.1:c.1161del NP_001393466.1:p.Gln388fs frameshift NM_001406538.1:c.1161del NP_001393467.1:p.Gln388fs frameshift NM_001406539.1:c.732del NP_001393468.1:p.Gln245fs frameshift NM_001406540.1:c.1161del NP_001393469.1:p.Gln388fs frameshift NM_001406541.1:c.1161del NP_001393470.1:p.Gln388fs frameshift NM_001406542.1:c.1161del NP_001393471.1:p.Gln388fs frameshift NM_001406543.1:c.1065del NP_001393472.1:p.Gln356fs frameshift NM_001406544.1:c.1065del NP_001393473.1:p.Gln356fs frameshift NM_001406545.1:c.1161del NP_001393474.1:p.Gln388fs frameshift NM_001406546.1:c.1161del NP_001393475.1:p.Gln388fs frameshift NM_001406547.1:c.1161del NP_001393476.1:p.Gln388fs frameshift NM_001406548.1:c.1161del NP_001393477.1:p.Gln388fs frameshift NC_000013.11:g.51974059del NC_000013.10:g.52548195del NG_008806.1:g.42436del - Protein change
- Q245fs, Q277fs, Q356fs, Q388fs
- Other names
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- Canonical SPDI
- NC_000013.11:51974058: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
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
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. |
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| ATP7B | - | - |
GRCh38 GRCh37 |
2916 | 3060 | |
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
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Feb 5, 2024 | RCV004016916.2 |
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. |
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Pathogenic
(Feb 05, 2024)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004834572.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
This variant deletes 1 nucleotide in exon 2 of the ATP7B gene, creating a frameshift and premature translation stop signal. This variant is expected to … (more)
This variant deletes 1 nucleotide in exon 2 of the ATP7B gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, this variant has not been reported in individuals affected with ATP7B-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of ATP7B function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. (less)
Number of individuals with the variant: 1
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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:
This variant deletes 1 nucleotide in exon 2 of the ATP7B gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, this variant has not been reported in individuals affected with ATP7B-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of ATP7B function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
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 May 08, 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.