NM_000053.4(ATP7B):c.2666A>T (p.His889Leu) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 28, 2023
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:: RCV003331799.1

Allele description [Variation Report for NM_000053.4(ATP7B):c.2666A>T (p.His889Leu)]

NM_000053.4(ATP7B):c.2666A>T (p.His889Leu)

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.2666A>T (p.His889Leu)

HGVS:

NC_000013.11:g.51950071T>A
NG_008806.1:g.66424A>T
NM_000053.4:c.2666A>TMANE SELECT
NM_001005918.3:c.2180A>T
NM_001243182.2:c.2333A>T
NM_001330578.2:c.2432A>T
NM_001330579.2:c.2414A>T
NM_001406511.1:c.2666A>T
NM_001406512.1:c.2666A>T
NM_001406513.1:c.2666A>T
NM_001406514.1:c.2633A>T
NM_001406515.1:c.2666A>T
NM_001406516.1:c.2666A>T
NM_001406517.1:c.2570A>T
NM_001406518.1:c.2570A>T
NM_001406519.1:c.2666A>T
NM_001406520.1:c.2522A>T
NM_001406521.1:c.2522A>T
NM_001406522.1:c.2522A>T
NM_001406523.1:c.2666A>T
NM_001406524.1:c.2489A>T
NM_001406525.1:c.2666A>T
NM_001406526.1:c.2666A>T
NM_001406527.1:c.2432A>T
NM_001406528.1:c.2432A>T
NM_001406530.1:c.2426A>T
NM_001406531.1:c.2414A>T
NM_001406532.1:c.2414A>T
NM_001406534.1:c.2432A>T
NM_001406535.1:c.2666A>T
NM_001406536.1:c.2336A>T
NM_001406537.1:c.2522A>T
NM_001406538.1:c.2432A>T
NM_001406539.1:c.2237A>T
NM_001406540.1:c.2414A>T
NM_001406541.1:c.2180A>T
NM_001406542.1:c.2180A>T
NM_001406543.1:c.2318A>T
NM_001406544.1:c.2084A>T
NM_001406545.1:c.2018A>T
NM_001406546.1:c.2180A>T
NM_001406547.1:c.2018A>T
NM_001406548.1:c.1376A>T
NP_000044.2:p.His889Leu
NP_001005918.1:p.His727Leu
NP_001230111.1:p.His778Leu
NP_001317507.1:p.His811Leu
NP_001317508.1:p.His805Leu
NP_001393440.1:p.His889Leu
NP_001393441.1:p.His889Leu
NP_001393442.1:p.His889Leu
NP_001393443.1:p.His878Leu
NP_001393444.1:p.His889Leu
NP_001393445.1:p.His889Leu
NP_001393446.1:p.His857Leu
NP_001393447.1:p.His857Leu
NP_001393448.1:p.His889Leu
NP_001393449.1:p.His841Leu
NP_001393450.1:p.His841Leu
NP_001393451.1:p.His841Leu
NP_001393452.1:p.His889Leu
NP_001393453.1:p.His830Leu
NP_001393454.1:p.His889Leu
NP_001393455.1:p.His889Leu
NP_001393456.1:p.His811Leu
NP_001393457.1:p.His811Leu
NP_001393459.1:p.His809Leu
NP_001393460.1:p.His805Leu
NP_001393461.1:p.His805Leu
NP_001393463.1:p.His811Leu
NP_001393464.1:p.His889Leu
NP_001393465.1:p.His779Leu
NP_001393466.1:p.His841Leu
NP_001393467.1:p.His811Leu
NP_001393468.1:p.His746Leu
NP_001393469.1:p.His805Leu
NP_001393470.1:p.His727Leu
NP_001393471.1:p.His727Leu
NP_001393472.1:p.His773Leu
NP_001393473.1:p.His695Leu
NP_001393474.1:p.His673Leu
NP_001393475.1:p.His727Leu
NP_001393476.1:p.His673Leu
NP_001393477.1:p.His459Leu
NC_000013.10:g.52524207T>A
NM_000053.3:c.2666A>T

Protein change:

H459L

Molecular consequence:

NM_000053.4:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.2180A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2333A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2432A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2414A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406511.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406512.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406513.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406514.1:c.2633A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406515.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406516.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406517.1:c.2570A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406518.1:c.2570A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406519.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406520.1:c.2522A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406521.1:c.2522A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406522.1:c.2522A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406523.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406524.1:c.2489A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406525.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406526.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406527.1:c.2432A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406528.1:c.2432A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406530.1:c.2426A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406531.1:c.2414A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406532.1:c.2414A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406534.1:c.2432A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406535.1:c.2666A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406536.1:c.2336A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406537.1:c.2522A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406538.1:c.2432A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406539.1:c.2237A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406540.1:c.2414A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406541.1:c.2180A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406542.1:c.2180A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406543.1:c.2318A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406544.1:c.2084A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406545.1:c.2018A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406546.1:c.2180A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406547.1:c.2018A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406548.1:c.1376A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004039465	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Aug 28, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004039465

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Aug 28, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004039465.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: ATP7B c.2666A>T (p.His889Leu) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 249584 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.2666A>T in individuals affected with Wilson Disease and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 7, 2023

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