NM_000053.4(ATP7B):c.1165C>G (p.Gln389Glu) AND Wilson disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 6, 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:: RCV004016731.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.1165C>G (p.Gln389Glu)]

NM_000053.4(ATP7B):c.1165C>G (p.Gln389Glu)

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.1165C>G (p.Gln389Glu)

HGVS:

NC_000013.11:g.51974055G>C
NG_008806.1:g.42440C>G
NM_000053.3:c.1165C>G
NM_000053.4:c.1165C>GMANE SELECT
NM_001005918.3:c.1165C>G
NM_001243182.2:c.832C>G
NM_001330578.2:c.1165C>G
NM_001330579.2:c.1165C>G
NM_001406511.1:c.1165C>G
NM_001406512.1:c.1165C>G
NM_001406513.1:c.1165C>G
NM_001406514.1:c.1165C>G
NM_001406515.1:c.1165C>G
NM_001406516.1:c.1165C>G
NM_001406517.1:c.1069C>G
NM_001406518.1:c.1069C>G
NM_001406519.1:c.1165C>G
NM_001406520.1:c.1165C>G
NM_001406521.1:c.1165C>G
NM_001406522.1:c.1165C>G
NM_001406523.1:c.1165C>G
NM_001406524.1:c.1165C>G
NM_001406525.1:c.1165C>G
NM_001406526.1:c.1165C>G
NM_001406527.1:c.1165C>G
NM_001406528.1:c.1165C>G
NM_001406530.1:c.1069C>G
NM_001406531.1:c.1165C>G
NM_001406532.1:c.1165C>G
NM_001406534.1:c.1165C>G
NM_001406535.1:c.1165C>G
NM_001406536.1:c.1069C>G
NM_001406537.1:c.1165C>G
NM_001406538.1:c.1165C>G
NM_001406539.1:c.736C>G
NM_001406540.1:c.1165C>G
NM_001406541.1:c.1165C>G
NM_001406542.1:c.1165C>G
NM_001406543.1:c.1069C>G
NM_001406544.1:c.1069C>G
NM_001406545.1:c.1165C>G
NM_001406546.1:c.1165C>G
NM_001406547.1:c.1165C>G
NM_001406548.1:c.1165C>G
NP_000044.2:p.Gln389Glu
NP_001005918.1:p.Gln389Glu
NP_001230111.1:p.Gln278Glu
NP_001317507.1:p.Gln389Glu
NP_001317508.1:p.Gln389Glu
NP_001393440.1:p.Gln389Glu
NP_001393441.1:p.Gln389Glu
NP_001393442.1:p.Gln389Glu
NP_001393443.1:p.Gln389Glu
NP_001393444.1:p.Gln389Glu
NP_001393445.1:p.Gln389Glu
NP_001393446.1:p.Gln357Glu
NP_001393447.1:p.Gln357Glu
NP_001393448.1:p.Gln389Glu
NP_001393449.1:p.Gln389Glu
NP_001393450.1:p.Gln389Glu
NP_001393451.1:p.Gln389Glu
NP_001393452.1:p.Gln389Glu
NP_001393453.1:p.Gln389Glu
NP_001393454.1:p.Gln389Glu
NP_001393455.1:p.Gln389Glu
NP_001393456.1:p.Gln389Glu
NP_001393457.1:p.Gln389Glu
NP_001393459.1:p.Gln357Glu
NP_001393460.1:p.Gln389Glu
NP_001393461.1:p.Gln389Glu
NP_001393463.1:p.Gln389Glu
NP_001393464.1:p.Gln389Glu
NP_001393465.1:p.Gln357Glu
NP_001393466.1:p.Gln389Glu
NP_001393467.1:p.Gln389Glu
NP_001393468.1:p.Gln246Glu
NP_001393469.1:p.Gln389Glu
NP_001393470.1:p.Gln389Glu
NP_001393471.1:p.Gln389Glu
NP_001393472.1:p.Gln357Glu
NP_001393473.1:p.Gln357Glu
NP_001393474.1:p.Gln389Glu
NP_001393475.1:p.Gln389Glu
NP_001393476.1:p.Gln389Glu
NP_001393477.1:p.Gln389Glu
NC_000013.10:g.52548191G>C

Protein change:

Q246E

Molecular consequence:

NM_000053.4:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.832C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406511.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406512.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406513.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406514.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406515.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406516.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406517.1:c.1069C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406518.1:c.1069C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406519.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406520.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406521.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406522.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406523.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406524.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406525.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406526.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406527.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406528.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406530.1:c.1069C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406531.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406532.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406534.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406535.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406536.1:c.1069C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406537.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406538.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406539.1:c.736C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406540.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406541.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406542.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406543.1:c.1069C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406544.1:c.1069C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406545.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406546.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406547.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406548.1:c.1165C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Wilson disease (WND)
Synonyms:: Wilson's disease; Hepatolenticular degeneration
Identifiers:: MONDO: MONDO:0010200; MedGen: C0019202; Orphanet: 905; OMIM: 277900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004839289	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Oct 6, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004839289

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Oct 6, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From All of Us Research Program, National Institutes of Health, SCV004839289.1

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

Description

This missense variant replaces glutamine with glutamic acid at codon 389 of the ATP7B protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. 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). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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