ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.732del (p.Asn244fs)
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.732del (p.Asn244fs)
Variation ID: 3234895 Accession: VCV003234895.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51974488 (GRCh38) [ NCBI UCSC ] 13: 52548624 (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 May 12, 2024 May 12, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.732del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Asn244fs frameshift NM_001005918.3:c.732del NP_001005918.1:p.Asn244fs frameshift NM_001243182.2:c.732del NP_001230111.1:p.Asn244fs frameshift NM_001330578.2:c.732del NP_001317507.1:p.Asn244fs frameshift NM_001330579.2:c.732del NP_001317508.1:p.Asn244fs frameshift NM_001406511.1:c.732del NP_001393440.1:p.Asn244fs frameshift NM_001406512.1:c.732del NP_001393441.1:p.Asn244fs frameshift NM_001406513.1:c.732del NP_001393442.1:p.Asn244fs frameshift NM_001406514.1:c.732del NP_001393443.1:p.Asn244fs frameshift NM_001406515.1:c.732del NP_001393444.1:p.Asn244fs frameshift NM_001406516.1:c.732del NP_001393445.1:p.Asn244fs frameshift NM_001406517.1:c.636del NP_001393446.1:p.Asn212fs frameshift NM_001406518.1:c.636del NP_001393447.1:p.Asn212fs frameshift NM_001406519.1:c.732del NP_001393448.1:p.Asn244fs frameshift NM_001406520.1:c.732del NP_001393449.1:p.Asn244fs frameshift NM_001406521.1:c.732del NP_001393450.1:p.Asn244fs frameshift NM_001406522.1:c.732del NP_001393451.1:p.Asn244fs frameshift NM_001406523.1:c.732del NP_001393452.1:p.Asn244fs frameshift NM_001406524.1:c.732del NP_001393453.1:p.Asn244fs frameshift NM_001406525.1:c.732del NP_001393454.1:p.Asn244fs frameshift NM_001406526.1:c.732del NP_001393455.1:p.Asn244fs frameshift NM_001406527.1:c.732del NP_001393456.1:p.Asn244fs frameshift NM_001406528.1:c.732del NP_001393457.1:p.Asn244fs frameshift NM_001406530.1:c.636del NP_001393459.1:p.Asn212fs frameshift NM_001406531.1:c.732del NP_001393460.1:p.Asn244fs frameshift NM_001406532.1:c.732del NP_001393461.1:p.Asn244fs frameshift NM_001406534.1:c.732del NP_001393463.1:p.Asn244fs frameshift NM_001406535.1:c.732del NP_001393464.1:p.Asn244fs frameshift NM_001406536.1:c.636del NP_001393465.1:p.Asn212fs frameshift NM_001406537.1:c.732del NP_001393466.1:p.Asn244fs frameshift NM_001406538.1:c.732del NP_001393467.1:p.Asn244fs frameshift NM_001406539.1:c.636del NP_001393468.1:p.Asn212fs frameshift NM_001406540.1:c.732del NP_001393469.1:p.Asn244fs frameshift NM_001406541.1:c.732del NP_001393470.1:p.Asn244fs frameshift NM_001406542.1:c.732del NP_001393471.1:p.Asn244fs frameshift NM_001406543.1:c.636del NP_001393472.1:p.Asn212fs frameshift NM_001406544.1:c.636del NP_001393473.1:p.Asn212fs frameshift NM_001406545.1:c.732del NP_001393474.1:p.Asn244fs frameshift NM_001406546.1:c.732del NP_001393475.1:p.Asn244fs frameshift NM_001406547.1:c.732del NP_001393476.1:p.Asn244fs frameshift NM_001406548.1:c.732del NP_001393477.1:p.Asn244fs frameshift NC_000013.11:g.51974488del NC_000013.10:g.52548624del NG_008806.1:g.42007del - Protein change
- N212fs, N244fs
- Other names
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- Canonical SPDI
- NC_000013.11:51974487:A:
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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 |
2901 | 3044 |
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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Likely pathogenic (1) |
criteria provided, single submitter
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- | RCV004547243.1 |
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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Likely pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV005042640.1
First in ClinVar: May 12, 2024 Last updated: May 12, 2024 |
Comment:
The frameshift c.732del p.Asn244LysfsTer18 variant in the ATP7B gene has not been reported previously as a pathogenic variant nor as a benign variant, to our … (more)
The frameshift c.732del p.Asn244LysfsTer18 variant in the ATP7B gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant causes a frameshift starting with codon Asparagine 244, changes this amino acid to Lysine residue, and creates a premature Stop codon at position 18 of the new reading frame, denoted p.Asn244LysfsTer18. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic. (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
HelpThere 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 19, 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.