NM_000053.4(ATP7B):c.1161del (p.Gln388fs) AND Wilson disease

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 5, 2024
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:: RCV004016916.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.1161del (p.Gln388fs)]

NM_000053.4(ATP7B):c.1161del (p.Gln388fs)

Gene:

ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q14.3

Genomic location:

Preferred name:

NM_000053.4(ATP7B):c.1161del (p.Gln388fs)

HGVS:

NC_000013.11:g.51974059del
NG_008806.1:g.42436del
NM_000053.4:c.1161delMANE SELECT
NM_001005918.3:c.1161del
NM_001243182.2:c.828del
NM_001330578.2:c.1161del
NM_001330579.2:c.1161del
NM_001406511.1:c.1161del
NM_001406512.1:c.1161del
NM_001406513.1:c.1161del
NM_001406514.1:c.1161del
NM_001406515.1:c.1161del
NM_001406516.1:c.1161del
NM_001406517.1:c.1065del
NM_001406518.1:c.1065del
NM_001406519.1:c.1161del
NM_001406520.1:c.1161del
NM_001406521.1:c.1161del
NM_001406522.1:c.1161del
NM_001406523.1:c.1161del
NM_001406524.1:c.1161del
NM_001406525.1:c.1161del
NM_001406526.1:c.1161del
NM_001406527.1:c.1161del
NM_001406528.1:c.1161del
NM_001406530.1:c.1065del
NM_001406531.1:c.1161del
NM_001406532.1:c.1161del
NM_001406534.1:c.1161del
NM_001406535.1:c.1161del
NM_001406536.1:c.1065del
NM_001406537.1:c.1161del
NM_001406538.1:c.1161del
NM_001406539.1:c.732del
NM_001406540.1:c.1161del
NM_001406541.1:c.1161del
NM_001406542.1:c.1161del
NM_001406543.1:c.1065del
NM_001406544.1:c.1065del
NM_001406545.1:c.1161del
NM_001406546.1:c.1161del
NM_001406547.1:c.1161del
NM_001406548.1:c.1161del
NP_000044.2:p.Gln388fs
NP_001005918.1:p.Gln388fs
NP_001230111.1:p.Gln277fs
NP_001317507.1:p.Gln388fs
NP_001317508.1:p.Gln388fs
NP_001393440.1:p.Gln388fs
NP_001393441.1:p.Gln388fs
NP_001393442.1:p.Gln388fs
NP_001393443.1:p.Gln388fs
NP_001393444.1:p.Gln388fs
NP_001393445.1:p.Gln388fs
NP_001393446.1:p.Gln356fs
NP_001393447.1:p.Gln356fs
NP_001393448.1:p.Gln388fs
NP_001393449.1:p.Gln388fs
NP_001393450.1:p.Gln388fs
NP_001393451.1:p.Gln388fs
NP_001393452.1:p.Gln388fs
NP_001393453.1:p.Gln388fs
NP_001393454.1:p.Gln388fs
NP_001393455.1:p.Gln388fs
NP_001393456.1:p.Gln388fs
NP_001393457.1:p.Gln388fs
NP_001393459.1:p.Gln356fs
NP_001393460.1:p.Gln388fs
NP_001393461.1:p.Gln388fs
NP_001393463.1:p.Gln388fs
NP_001393464.1:p.Gln388fs
NP_001393465.1:p.Gln356fs
NP_001393466.1:p.Gln388fs
NP_001393467.1:p.Gln388fs
NP_001393468.1:p.Gln245fs
NP_001393469.1:p.Gln388fs
NP_001393470.1:p.Gln388fs
NP_001393471.1:p.Gln388fs
NP_001393472.1:p.Gln356fs
NP_001393473.1:p.Gln356fs
NP_001393474.1:p.Gln388fs
NP_001393475.1:p.Gln388fs
NP_001393476.1:p.Gln388fs
NP_001393477.1:p.Gln388fs
NC_000013.10:g.52548195del

Protein change:

Q245fs

Molecular consequence:

NM_000053.4:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001005918.3:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243182.2:c.828del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330578.2:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330579.2:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406511.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406512.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406513.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406514.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406515.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406516.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406517.1:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406518.1:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406519.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406520.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406521.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406522.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406523.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406524.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406525.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406526.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406527.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406528.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406530.1:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406531.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406532.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406534.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406535.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406536.1:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406537.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406538.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406539.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406540.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406541.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406542.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406543.1:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406544.1:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406545.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406546.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406547.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406548.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004834572	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 5, 2024)	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

SCV004834572

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 5, 2024)

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, SCV004834572.1

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

Description

This variant deletes 1 nucleotide in exon 2 of the ATP7B gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, 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). Loss of ATP7B function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

#	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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