NM_000053.4(ATP7B):c.3182G>A (p.Gly1061Glu) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 24, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001558379.7

Allele description [Variation Report for NM_000053.4(ATP7B):c.3182G>A (p.Gly1061Glu)]

NM_000053.4(ATP7B):c.3182G>A (p.Gly1061Glu)

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.3182G>A (p.Gly1061Glu)

HGVS:

NC_000013.11:g.51944170C>T
NG_008806.1:g.72325G>A
NM_000053.4:c.3182G>AMANE SELECT
NM_001005918.3:c.2561G>A
NM_001243182.2:c.2849G>A
NM_001330578.2:c.2948G>A
NM_001330579.2:c.2930G>A
NP_000044.2:p.Gly1061Glu
NP_001005918.1:p.Gly854Glu
NP_001230111.1:p.Gly950Glu
NP_001317507.1:p.Gly983Glu
NP_001317508.1:p.Gly977Glu
NC_000013.10:g.52518306C>T
NM_000053.2:c.3182G>A
NM_000053.3:c.3182G>A
NM_000053.3:c.[3182G>A]
NM_001005918.2:c.2561G>A
P35670:p.Gly1061Glu

Protein change:

G1061E

Links:

UniProtKB: P35670#VAR_009017; dbSNP: rs764131178

NCBI 1000 Genomes Browser:

rs764131178

Molecular consequence:

NM_000053.4:c.3182G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.2561G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2849G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2948G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2930G>A - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

variation affecting protein function [Variation Ontology: 0003]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001780314	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 16, 2021)	germline	clinical testing	Citation Link,
SCV002525816	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 24, 2021)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 32778786, 31059521, 30212743, 30120852, 27982432, 25982861, 24661374, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001780314

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 16, 2021)

germline

clinical testing

Citation Link,

SCV002525816

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 24, 2021)

germline

clinical testing

PubMed (8)
[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	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Analysis of Wilson disease mutations revealed that interactions between different ATP7B mutants modify their properties.

Roy S, McCann CJ, Ralle M, Ray K, Ray J, Lutsenko S, Jayakanthan S.

Sci Rep. 2020 Aug 10;10(1):13487. doi: 10.1038/s41598-020-70366-7.

PubMed [citation]

PMID:: 32778786
PMCID:: PMC7418023

Genetic analysis of ATP7B in 102 south Indian families with Wilson disease.

Singh N, Kallollimath P, Shah MH, Kapoor S, Bhat VK, Viswanathan LG, Nagappa M, Bindu PS, Taly AB, Sinha S, Kumar A.

PLoS One. 2019;14(5):e0215779. doi: 10.1371/journal.pone.0215779.

PubMed [citation]

PMID:: 31059521
PMCID:: PMC6502322

See all PubMed Citations (8)

Details of each submission

From GeneDx, SCV001780314.1

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

Description

Found on 11% of Wilson disease patient chromosomes in the Indian population (Gupta et al., 2007); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 10502777, 22692182, 25982861, 33083013, 31589614, 24094725, 23430908, 18371106, 26207595, 17634212, 25900946, 17823867, 17264425, 15952988, 30120852, 15024742, 10544227)

#	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		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV002525816.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

PS4, PS3, PM1, PM2, PP3, PP4

#	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: Sep 29, 2024

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