NM_000053.4(ATP7B):c.628A>G (p.Ile210Val) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(2) (Last evaluated: Oct 11, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000436240.5

Allele description [Variation Report for NM_000053.4(ATP7B):c.628A>G (p.Ile210Val)]

NM_000053.4(ATP7B):c.628A>G (p.Ile210Val)

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.628A>G (p.Ile210Val)
HGVS:
  • NC_000013.11:g.51974592T>C
  • NG_008806.1:g.41903A>G
  • NM_000053.4:c.628A>GMANE SELECT
  • NM_001005918.3:c.628A>G
  • NM_001243182.1:c.628A>G
  • NM_001330578.1:c.628A>G
  • NM_001330579.2:c.628A>G
  • NP_000044.2:p.Ile210Val
  • NP_000044.2:p.Ile210Val
  • NP_001005918.1:p.Ile210Val
  • NP_001230111.1:p.Ile210Val
  • NP_001317507.1:p.Ile210Val
  • NP_001317508.1:p.Ile210Val
  • NC_000013.10:g.52548728T>C
  • NM_000053.2:c.628A>G
  • NM_000053.3:c.628A>G
Protein change:
I210V
Links:
dbSNP: rs61733680
NCBI 1000 Genomes Browser:
rs61733680
Molecular consequence:
  • NM_000053.4:c.628A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005918.3:c.628A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243182.1:c.628A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330578.1:c.628A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330579.2:c.628A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000109893EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Feb 26, 2013)
germlineclinical testing

Citation Link,

SCV000510651Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicscriteria provided, single submitter
Likely Benign
(Oct 11, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000694469Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Jun 15, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001812199GeneDxno assertion criteria provided
Likely benign
(Jun 22, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing

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 EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000109893.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics, SCV000510651.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Converted during submission to Likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.001228not providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694469.1

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

Description

Variant summary: The ATP7B c.628A>G (p.Ile210Val) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome (SNPs&GO not captured due to low reliability index. This variant was found in 75/120704 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0066394 (65/9790). This frequency is slightly greater than the estimated maximal expected allele frequency of a pathogenic ATP7B variant (0.0054006), suggesting this is variant may be a benign polymorphism found primarily in the populations of African origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications, nor evaluated for functional impact by in vivo/vitro studies. In addition, one clinical diagnostic laboratory classified this variant as a VUS. Because of the absence of clinical information and the lack of functional studies, the variant was classified as a variant of uncertain significance (VUS)-possibly benign until additional information becomes available.

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

From GeneDx, SCV001812199.1

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

Last Updated: Sep 18, 2021

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