NM_000053.4(ATP7B):c.1947-4C>T AND not specified

Clinical significance:Uncertain significance (Last evaluated: Oct 5, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000440735.3

Allele description [Variation Report for NM_000053.4(ATP7B):c.1947-4C>T]

NM_000053.4(ATP7B):c.1947-4C>T

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.1947-4C>T
HGVS:
  • NC_000013.11:g.51960326G>A
  • NG_008806.1:g.56169C>T
  • NM_000053.4:c.1947-4C>TMANE SELECT
  • NM_001005918.3:c.1870-2719C>T
  • NM_001243182.2:c.1614-4C>T
  • NM_001330578.2:c.1947-4C>T
  • NM_001330579.2:c.1870-1782C>T
  • NC_000013.10:g.52534462G>A
  • NM_000053.3:c.1947-4C>T
Links:
dbSNP: rs74904335
NCBI 1000 Genomes Browser:
rs74904335
Molecular consequence:
  • NM_000053.4:c.1947-4C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001005918.3:c.1870-2719C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001243182.2:c.1614-4C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330578.2:c.1947-4C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330579.2:c.1870-1782C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000918584Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Uncertain significance
(Oct 5, 2017)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

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

Citations

PubMed

Mutational analysis of ATP7B and genotype-phenotype correlation in Japanese with Wilson's disease.

Okada T, Shiono Y, Hayashi H, Satoh H, Sawada T, Suzuki A, Takeda Y, Yano M, Michitaka K, Onji M, Mabuchi H.

Hum Mutat. 2000;15(5):454-62.

PubMed [citation]
PMID:
10790207

Identification of three novel mutations and a high frequency of the Arg778Leu mutation in Korean patients with Wilson disease.

Kim EK, Yoo OJ, Song KY, Yoo HW, Choi SY, Cho SW, Hahn SH.

Hum Mutat. 1998;11(4):275-8.

PubMed [citation]
PMID:
9554743

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918584.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: The ATP7B c.1947-4C>T variant causes a missense change involving the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 159/275932 control chromosomes including two homozygous occurrences (gnomAD), predominantly observed in the East Asian subpopulation at a frequency of 0.008075 (152/18824). This frequency is about 1.5 times the estimated maximal expected allele frequency of a pathogenic ATP7B variant (0.0054006), suggesting this is possibly a benign rare polymorphism found primarily in the populations of East Asian origin. Two studies report this variant as a polymorphism, without clearly stating if it was found in WD patients or controls (Kim_1998, Kim_1998). One clinical diagnostic laboratory has classified this variant as likely benign. Taken together, this variant is classified as VUS-possibly benign.

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

Last Updated: Nov 27, 2021

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