NM_000053.4(ATP7B):c.3074T>A (p.Met1025Lys) AND Wilson disease

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 1, 2021
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:: RCV001507001.1

Allele description [Variation Report for NM_000053.4(ATP7B):c.3074T>A (p.Met1025Lys)]

NM_000053.4(ATP7B):c.3074T>A (p.Met1025Lys)

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.3074T>A (p.Met1025Lys)

HGVS:

NC_000013.11:g.51944278A>T
NG_008806.1:g.72217T>A
NM_000053.4:c.3074T>AMANE SELECT
NM_001005918.3:c.2453T>A
NM_001243182.2:c.2741T>A
NM_001330578.2:c.2840T>A
NM_001330579.2:c.2822T>A
NP_000044.2:p.Met1025Lys
NP_001005918.1:p.Met818Lys
NP_001230111.1:p.Met914Lys
NP_001317507.1:p.Met947Lys
NP_001317508.1:p.Met941Lys
NC_000013.10:g.52518414A>T
NM_000053.3:c.3074T>A
p.Met1025Lys

Protein change:

M1025K

Links:

dbSNP: rs1555286633

NCBI 1000 Genomes Browser:

rs1555286633

Molecular consequence:

NM_000053.4:c.3074T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.2453T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2741T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2840T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2822T>A - 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
SCV001711924	Inborn Errors of Metabolism Laboratory, Hospices Civils de Lyon	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 1, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18034201, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001711924

Inborn Errors of Metabolism Laboratory, Hospices Civils de Lyon

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 1, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutational analysis of 65 Wilson disease patients in Hong Kong Chinese: identification of 17 novel mutations and its genetic heterogeneity.

Mak CM, Lam CW, Tam S, Lai CL, Chan LY, Fan ST, Lau YL, Lai JY, Yuen P, Hui J, Fu CC, Wong KS, Mak WL, Tze K, Tong SF, Lau A, Leung N, Hui A, Cheung KM, Ko CH, Chan YK, Ma O, et al.

J Hum Genet. 2008;53(1):55-63. doi: 10.1007/s10038-007-0218-2. Epub 2007 Nov 22. Erratum in: J Hum Genet. 2008;53(4):375. Lai, Jak-Yiu [corrected to Lai, Sik-To]. J Hum Genet. 2008 Apr;53(4):375. doi: 10.1007/s10038-007-0244-0.

PubMed [citation]

PMID:: 18034201

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 Inborn Errors of Metabolism Laboratory, Hospices Civils de Lyon, SCV001711924.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

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

Last Updated: Dec 24, 2023

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