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NM_000053.4(ATP7B):c.3403G>A (p.Ala1135Thr) AND not provided

Germline classification:
Benign/Likely benign (3 submissions)
Last evaluated:
Mar 1, 2024
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:
RCV000757024.33

Allele description [Variation Report for NM_000053.4(ATP7B):c.3403G>A (p.Ala1135Thr)]

NM_000053.4(ATP7B):c.3403G>A (p.Ala1135Thr)

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.3403G>A (p.Ala1135Thr)
HGVS:
  • NC_000013.11:g.51942395C>T
  • NG_008806.1:g.74100G>A
  • NM_000053.4:c.3403G>AMANE SELECT
  • NM_001005918.3:c.2782G>A
  • NM_001243182.2:c.3070G>A
  • NM_001330578.2:c.3169G>A
  • NM_001330579.2:c.3151G>A
  • NP_000044.2:p.Ala1135Thr
  • NP_001005918.1:p.Ala928Thr
  • NP_001230111.1:p.Ala1024Thr
  • NP_001317507.1:p.Ala1057Thr
  • NP_001317508.1:p.Ala1051Thr
  • NC_000013.10:g.52516531C>T
  • NM_000053.3:c.3403G>A
  • NM_001005918.2:c.2782G>A
Protein change:
A1024T
Links:
dbSNP: rs187200982
NCBI 1000 Genomes Browser:
rs187200982
Molecular consequence:
  • NM_000053.4:c.3403G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005918.3:c.2782G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243182.2:c.3070G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330578.2:c.3169G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330579.2:c.3151G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
6

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000885052ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)
Benign
(May 2, 2017)
germlineclinical testing

Citation Link,

SCV000980373GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Jun 18, 2018)
germlineclinical testing

Citation Link,

SCV001156168CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Mar 1, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes6not providednot providednot providednot providedclinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000885052.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV000980373.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV001156168.27

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided6not providednot providedclinical testingnot provided

Description

ATP7B: BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided6not providednot providednot provided

Last Updated: Oct 20, 2024