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NM_000053.4(ATP7B):c.1908dup (p.Asn637fs) AND Wilson disease

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Sep 22, 2023
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:
RCV003464938.3

Allele description [Variation Report for NM_000053.4(ATP7B):c.1908dup (p.Asn637fs)]

NM_000053.4(ATP7B):c.1908dup (p.Asn637fs)

Gene:
ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
13q14.3
Genomic location:
Preferred name:
NM_000053.4(ATP7B):c.1908dup (p.Asn637fs)
HGVS:
  • NC_000013.11:g.51961878dup
  • NG_008806.1:g.54620dup
  • NM_000053.4:c.1908dupMANE SELECT
  • NM_001005918.3:c.1869+2997dup
  • NM_001243182.2:c.1575dup
  • NM_001330578.2:c.1908dup
  • NM_001330579.2:c.1869+2997dup
  • NM_001406511.1:c.1908dup
  • NM_001406512.1:c.1908dup
  • NM_001406513.1:c.1908dup
  • NM_001406514.1:c.1875dup
  • NM_001406515.1:c.1908dup
  • NM_001406516.1:c.1908dup
  • NM_001406517.1:c.1812dup
  • NM_001406518.1:c.1812dup
  • NM_001406519.1:c.1908dup
  • NM_001406520.1:c.1908dup
  • NM_001406521.1:c.1908dup
  • NM_001406522.1:c.1908dup
  • NM_001406523.1:c.1908dup
  • NM_001406524.1:c.1875dup
  • NM_001406525.1:c.1908dup
  • NM_001406526.1:c.1908dup
  • NM_001406527.1:c.1908dup
  • NM_001406528.1:c.1908dup
  • NM_001406530.1:c.1812dup
  • NM_001406531.1:c.1869+2997dup
  • NM_001406532.1:c.1869+2997dup
  • NM_001406534.1:c.1908dup
  • NM_001406535.1:c.1908dup
  • NM_001406536.1:c.1812dup
  • NM_001406537.1:c.1908dup
  • NM_001406538.1:c.1908dup
  • NM_001406539.1:c.1479dup
  • NM_001406540.1:c.1869+2997dup
  • NM_001406541.1:c.1869+2997dup
  • NM_001406542.1:c.1869+2997dup
  • NM_001406543.1:c.1773+2997dup
  • NM_001406544.1:c.1773+2997dup
  • NM_001406545.1:c.1708-4268dup
  • NM_001406546.1:c.1869+2997dup
  • NM_001406547.1:c.1708-4268dup
  • NM_001406548.1:c.1286-11714dup
  • NP_000044.2:p.Asn637fs
  • NP_001230111.1:p.Asn526fs
  • NP_001317507.1:p.Asn637fs
  • NP_001393440.1:p.Asn637fs
  • NP_001393441.1:p.Asn637fs
  • NP_001393442.1:p.Asn637fs
  • NP_001393443.1:p.Asn626fs
  • NP_001393444.1:p.Asn637fs
  • NP_001393445.1:p.Asn637fs
  • NP_001393446.1:p.Asn605fs
  • NP_001393447.1:p.Asn605fs
  • NP_001393448.1:p.Asn637fs
  • NP_001393449.1:p.Asn637fs
  • NP_001393450.1:p.Asn637fs
  • NP_001393451.1:p.Asn637fs
  • NP_001393452.1:p.Asn637fs
  • NP_001393453.1:p.Asn626fs
  • NP_001393454.1:p.Asn637fs
  • NP_001393455.1:p.Asn637fs
  • NP_001393456.1:p.Asn637fs
  • NP_001393457.1:p.Asn637fs
  • NP_001393459.1:p.Asn605fs
  • NP_001393463.1:p.Asn637fs
  • NP_001393464.1:p.Asn637fs
  • NP_001393465.1:p.Asn605fs
  • NP_001393466.1:p.Asn637fs
  • NP_001393467.1:p.Asn637fs
  • NP_001393468.1:p.Asn494fs
  • NC_000013.10:g.52536010_52536011insG
  • NC_000013.10:g.52536014dup
Protein change:
N494fs
Molecular consequence:
  • NM_000053.4:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001243182.2:c.1575dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330578.2:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406511.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406512.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406513.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406514.1:c.1875dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406515.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406516.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406517.1:c.1812dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406518.1:c.1812dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406519.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406520.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406521.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406522.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406523.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406524.1:c.1875dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406525.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406526.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406527.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406528.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406530.1:c.1812dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406534.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406535.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406536.1:c.1812dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406537.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406538.1:c.1908dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406539.1:c.1479dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001005918.3:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330579.2:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406531.1:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406532.1:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406540.1:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406541.1:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406542.1:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406543.1:c.1773+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406544.1:c.1773+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406545.1:c.1708-4268dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406546.1:c.1869+2997dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406547.1:c.1708-4268dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406548.1:c.1286-11714dup - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Wilson disease (WND)
Synonyms:
Wilson's disease; Hepatolenticular degeneration
Identifiers:
MONDO: MONDO:0010200; MedGen: C0019202; Orphanet: 905; OMIM: 277900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004216393Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jun 24, 2023)
unknownclinical testing

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

SCV004325309Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Sep 22, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

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

Null mutation of the murine ATP7B (Wilson disease) gene results in intracellular copper accumulation and late-onset hepatic nodular transformation.

Buiakova OI, Xu J, Lutsenko S, Zeitlin S, Das K, Das S, Ross BM, Mekios C, Scheinberg IH, Gilliam TC.

Hum Mol Genet. 1999 Sep;8(9):1665-71.

PubMed [citation]
PMID:
10441329
See all PubMed Citations (4)

Details of each submission

From Baylor Genetics, SCV004216393.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004325309.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Asn637Glnfs*118) in the ATP7B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ATP7B-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024