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NM_000053.4(ATP7B):c.3498T>C (p.Ser1166=) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 25, 2020
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:
RCV002453467.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.3498T>C (p.Ser1166=)]

NM_000053.4(ATP7B):c.3498T>C (p.Ser1166=)

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.3498T>C (p.Ser1166=)
HGVS:
  • NC_000013.11:g.51941139A>G
  • NG_008806.1:g.75356T>C
  • NM_000053.4:c.3498T>CMANE SELECT
  • NM_001005918.3:c.2877T>C
  • NM_001243182.2:c.3165T>C
  • NM_001330578.2:c.3264T>C
  • NM_001330579.2:c.3246T>C
  • NP_000044.2:p.Ser1166=
  • NP_001005918.1:p.Ser959=
  • NP_001230111.1:p.Ser1055=
  • NP_001317507.1:p.Ser1088=
  • NP_001317508.1:p.Ser1082=
  • NC_000013.10:g.52515275A>G
  • NM_000053.3:c.3498T>C
Links:
dbSNP: rs587783314
NCBI 1000 Genomes Browser:
rs587783314
Molecular consequence:
  • NM_000053.4:c.3498T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001005918.3:c.2877T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001243182.2:c.3165T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330578.2:c.3264T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330579.2:c.3246T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002612912Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Aug 25, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002612912.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Oct 13, 2024