NM_000053.4(ATP7B):c.2855G>A (p.Arg952Lys) AND not provided

Germline classification:: Benign (2 submissions)
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:: RCV001357476.10

Allele description [Variation Report for NM_000053.4(ATP7B):c.2855G>A (p.Arg952Lys)]

NM_000053.4(ATP7B):c.2855G>A (p.Arg952Lys)

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.2855G>A (p.Arg952Lys)

HGVS:

NC_000013.11:g.51949672C>T
NG_008806.1:g.66823G>A
NM_000053.4:c.2855G>AMANE SELECT
NM_001005918.3:c.2244+335G>A
NM_001243182.2:c.2522G>A
NM_001330578.2:c.2621G>A
NM_001330579.2:c.2603G>A
NP_000044.2:p.Arg952Lys
NP_000044.2:p.Arg952Lys
NP_001230111.1:p.Arg841Lys
NP_001317507.1:p.Arg874Lys
NP_001317508.1:p.Arg868Lys
NC_000013.10:g.52523808C>T
NM_000053.3:c.2855G>A
NM_001005918.2:c.2244+335G>A
P35670:p.Arg952Lys

Protein change:

R841K

Links:

UniProtKB: P35670#VAR_000746; dbSNP: rs732774

NCBI 1000 Genomes Browser:

rs732774

Molecular consequence:

NM_001005918.3:c.2244+335G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000053.4:c.2855G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2522G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2621G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2603G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001552958	Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR) See additional submitters Franklin by Genoox	no assertion criteria provided	Uncertain significance	unknown	clinical testing
SCV005230373	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001552958

Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided

Uncertain significance

unknown

clinical testing

SCV005230373

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

not provided

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	not provided

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 Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001552958.1

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

Description

multiple AR variants in same gene - keep for nowAllele frequency is common in at least one population database (frequency: 64.047% in ExAC) based on the frequency threshold of 2.434% for this gene.Variant was observed in a homozygous state in population databases more than expected for disease.

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

From Breakthrough Genomics, Breakthrough Genomics, SCV005230373.1

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

#	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

Last Updated: Oct 13, 2024

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