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NM_000053.4(ATP7B):c.2876A>T (p.Lys959Met) AND Inborn genetic diseases

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 27, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002437724.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.2876A>T (p.Lys959Met)]

NM_000053.4(ATP7B):c.2876A>T (p.Lys959Met)

Gene:
ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q14.3
Genomic location:
Preferred name:
NM_000053.4(ATP7B):c.2876A>T (p.Lys959Met)
HGVS:
  • NC_000013.11:g.51946468T>A
  • NG_008806.1:g.70027A>T
  • NM_000053.4:c.2876A>TMANE SELECT
  • NM_001005918.3:c.2255A>T
  • NM_001243182.2:c.2543A>T
  • NM_001330578.2:c.2642A>T
  • NM_001330579.2:c.2624A>T
  • NM_001406511.1:c.2876A>T
  • NM_001406512.1:c.2876A>T
  • NM_001406513.1:c.2876A>T
  • NM_001406514.1:c.2843A>T
  • NM_001406515.1:c.2822A>T
  • NM_001406516.1:c.2822A>T
  • NM_001406517.1:c.2780A>T
  • NM_001406518.1:c.2780A>T
  • NM_001406519.1:c.2741A>T
  • NM_001406520.1:c.2732A>T
  • NM_001406521.1:c.2732A>T
  • NM_001406522.1:c.2732A>T
  • NM_001406523.1:c.2876A>T
  • NM_001406524.1:c.2699A>T
  • NM_001406526.1:c.2876A>T
  • NM_001406527.1:c.2642A>T
  • NM_001406528.1:c.2642A>T
  • NM_001406530.1:c.2636A>T
  • NM_001406531.1:c.2624A>T
  • NM_001406532.1:c.2624A>T
  • NM_001406534.1:c.2588A>T
  • NM_001406536.1:c.2546A>T
  • NM_001406538.1:c.2642A>T
  • NM_001406539.1:c.2447A>T
  • NM_001406541.1:c.2390A>T
  • NM_001406542.1:c.2390A>T
  • NM_001406543.1:c.2528A>T
  • NM_001406544.1:c.2294A>T
  • NM_001406545.1:c.2228A>T
  • NM_001406548.1:c.1586A>T
  • NP_000044.2:p.Lys959Met
  • NP_001005918.1:p.Lys752Met
  • NP_001230111.1:p.Lys848Met
  • NP_001317507.1:p.Lys881Met
  • NP_001317508.1:p.Lys875Met
  • NP_001393440.1:p.Lys959Met
  • NP_001393441.1:p.Lys959Met
  • NP_001393442.1:p.Lys959Met
  • NP_001393443.1:p.Lys948Met
  • NP_001393444.1:p.Lys941Met
  • NP_001393445.1:p.Lys941Met
  • NP_001393446.1:p.Lys927Met
  • NP_001393447.1:p.Lys927Met
  • NP_001393448.1:p.Lys914Met
  • NP_001393449.1:p.Lys911Met
  • NP_001393450.1:p.Lys911Met
  • NP_001393451.1:p.Lys911Met
  • NP_001393452.1:p.Lys959Met
  • NP_001393453.1:p.Lys900Met
  • NP_001393455.1:p.Lys959Met
  • NP_001393456.1:p.Lys881Met
  • NP_001393457.1:p.Lys881Met
  • NP_001393459.1:p.Lys879Met
  • NP_001393460.1:p.Lys875Met
  • NP_001393461.1:p.Lys875Met
  • NP_001393463.1:p.Lys863Met
  • NP_001393465.1:p.Lys849Met
  • NP_001393467.1:p.Lys881Met
  • NP_001393468.1:p.Lys816Met
  • NP_001393470.1:p.Lys797Met
  • NP_001393471.1:p.Lys797Met
  • NP_001393472.1:p.Lys843Met
  • NP_001393473.1:p.Lys765Met
  • NP_001393474.1:p.Lys743Met
  • NP_001393477.1:p.Lys529Met
  • NC_000013.10:g.52520604T>A
  • NM_000053.3:c.2876A>T
Protein change:
K529M
Molecular consequence:
  • NM_000053.4:c.2876A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005918.3:c.2255A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243182.2:c.2543A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330578.2:c.2642A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330579.2:c.2624A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406511.1:c.2876A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406512.1:c.2876A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406513.1:c.2876A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406514.1:c.2843A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406515.1:c.2822A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406516.1:c.2822A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406517.1:c.2780A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406518.1:c.2780A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406519.1:c.2741A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406520.1:c.2732A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406521.1:c.2732A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406522.1:c.2732A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406523.1:c.2876A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406524.1:c.2699A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406526.1:c.2876A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406527.1:c.2642A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406528.1:c.2642A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406530.1:c.2636A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406531.1:c.2624A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406532.1:c.2624A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406534.1:c.2588A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406536.1:c.2546A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406538.1:c.2642A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406539.1:c.2447A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406541.1:c.2390A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406542.1:c.2390A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406543.1:c.2528A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406544.1:c.2294A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406545.1:c.2228A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406548.1:c.1586A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002745943Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(May 27, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV002745943.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024