ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.2876A>T (p.Lys959Met)
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
-
NM_000053.4(ATP7B):c.2876A>T (p.Lys959Met)
Variation ID: 1797099 Accession: VCV001797099.2
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 13q14.3 13: 51946468 (GRCh38) [ NCBI UCSC ] 13: 52520604 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 29, 2022 May 1, 2024 May 27, 2022 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000053.4:c.2876A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Lys959Met missense NM_001005918.3:c.2255A>T NP_001005918.1:p.Lys752Met missense NM_001243182.2:c.2543A>T NP_001230111.1:p.Lys848Met missense NM_001330578.2:c.2642A>T NP_001317507.1:p.Lys881Met missense NM_001330579.2:c.2624A>T NP_001317508.1:p.Lys875Met missense NM_001406511.1:c.2876A>T NP_001393440.1:p.Lys959Met missense NM_001406512.1:c.2876A>T NP_001393441.1:p.Lys959Met missense NM_001406513.1:c.2876A>T NP_001393442.1:p.Lys959Met missense NM_001406514.1:c.2843A>T NP_001393443.1:p.Lys948Met missense NM_001406515.1:c.2822A>T NP_001393444.1:p.Lys941Met missense NM_001406516.1:c.2822A>T NP_001393445.1:p.Lys941Met missense NM_001406517.1:c.2780A>T NP_001393446.1:p.Lys927Met missense NM_001406518.1:c.2780A>T NP_001393447.1:p.Lys927Met missense NM_001406519.1:c.2741A>T NP_001393448.1:p.Lys914Met missense NM_001406520.1:c.2732A>T NP_001393449.1:p.Lys911Met missense NM_001406521.1:c.2732A>T NP_001393450.1:p.Lys911Met missense NM_001406522.1:c.2732A>T NP_001393451.1:p.Lys911Met missense NM_001406523.1:c.2876A>T NP_001393452.1:p.Lys959Met missense NM_001406524.1:c.2699A>T NP_001393453.1:p.Lys900Met missense NM_001406526.1:c.2876A>T NP_001393455.1:p.Lys959Met missense NM_001406527.1:c.2642A>T NP_001393456.1:p.Lys881Met missense NM_001406528.1:c.2642A>T NP_001393457.1:p.Lys881Met missense NM_001406530.1:c.2636A>T NP_001393459.1:p.Lys879Met missense NM_001406531.1:c.2624A>T NP_001393460.1:p.Lys875Met missense NM_001406532.1:c.2624A>T NP_001393461.1:p.Lys875Met missense NM_001406534.1:c.2588A>T NP_001393463.1:p.Lys863Met missense NM_001406536.1:c.2546A>T NP_001393465.1:p.Lys849Met missense NM_001406538.1:c.2642A>T NP_001393467.1:p.Lys881Met missense NM_001406539.1:c.2447A>T NP_001393468.1:p.Lys816Met missense NM_001406541.1:c.2390A>T NP_001393470.1:p.Lys797Met missense NM_001406542.1:c.2390A>T NP_001393471.1:p.Lys797Met missense NM_001406543.1:c.2528A>T NP_001393472.1:p.Lys843Met missense NM_001406544.1:c.2294A>T NP_001393473.1:p.Lys765Met missense NM_001406545.1:c.2228A>T NP_001393474.1:p.Lys743Met missense NM_001406548.1:c.1586A>T NP_001393477.1:p.Lys529Met missense NC_000013.11:g.51946468T>A NC_000013.10:g.52520604T>A NG_008806.1:g.70027A>T - Protein change
- K765M, K848M, K879M, K881M, K941M, K816M, K843M, K863M, K900M, K911M, K927M, K948M, K959M, K529M, K743M, K849M, K914M, K752M, K797M, K875M
- Other names
- -
- Canonical SPDI
- NC_000013.11:51946467:T:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
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.
-
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
- 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. |
|||
ATP7B | - | - |
GRCh38 GRCh37 |
2893 | 3035 |
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. |
---|---|---|---|---|
Uncertain significance (1) |
criteria provided, single submitter
|
May 27, 2022 | RCV002437724.2 |
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. |
|
---|---|---|---|---|---|
Uncertain significance
(May 27, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV002745943.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.K959M variant (also known as c.2876A>T), located in coding exon 13 of the ATP7B gene, results from an A to T substitution at nucleotide … (more)
The p.K959M variant (also known as c.2876A>T), located in coding exon 13 of the ATP7B gene, results from an A to T substitution at nucleotide position 2876. The lysine at codon 959 is replaced by methionine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)
|
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 01, 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.