NM_000053.4(ATP7B):c.3784G>T (p.Val1262Phe) AND Wilson disease

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Aug 10, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000665788.4

Allele description [Variation Report for NM_000053.4(ATP7B):c.3784G>T (p.Val1262Phe)]

NM_000053.4(ATP7B):c.3784G>T (p.Val1262Phe)

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.3784G>T (p.Val1262Phe)
HGVS:
  • NC_000013.11:g.51937595C>A
  • NG_008806.1:g.78900G>T
  • NM_000053.4:c.3784G>TMANE SELECT
  • NM_001005918.3:c.3163G>T
  • NM_001243182.2:c.3451G>T
  • NM_001330578.2:c.3550G>T
  • NM_001330579.2:c.3532G>T
  • NP_000044.2:p.Val1262Phe
  • NP_001005918.1:p.Val1055Phe
  • NP_001230111.1:p.Val1151Phe
  • NP_001317507.1:p.Val1184Phe
  • NP_001317508.1:p.Val1178Phe
  • NC_000013.10:g.52511731C>A
  • NM_000053.3:c.3784G>T
Protein change:
V1055F
Links:
dbSNP: rs769484789
NCBI 1000 Genomes Browser:
rs769484789
Molecular consequence:
  • NM_000053.4:c.3784G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005918.3:c.3163G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243182.2:c.3451G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330578.2:c.3550G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330579.2:c.3532G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000789962Counsylcriteria provided, single submitter
Likely pathogenic
(Mar 1, 2017)
unknownclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Citation Link,

SCV001235665Invitaecriteria provided, single submitter
Pathogenic
(Sep 20, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV001977234Nilou-Genome Labcriteria provided, single submitter
Likely pathogenic
(Aug 10, 2021)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

The Challenges of Diagnosing and Following Wilson Disease in the Presence of Proteinuria.

Khan S, Schilsky M, Silber G, Morgenstern B, Miloh T.

Pediatr Gastroenterol Hepatol Nutr. 2016 Jun;19(2):139-42. doi: 10.5223/pghn.2016.19.2.139. Epub 2016 Jun 28.

PubMed [citation]
PMID:
27437191
PMCID:
PMC4942312

Outcome and development of symptoms after orthotopic liver transplantation for Wilson disease.

Weiss KH, Schäfer M, Gotthardt DN, Angerer A, Mogler C, Schirmacher P, Schemmer P, Stremmel W, Sauer P.

Clin Transplant. 2013 Nov-Dec;27(6):914-22. doi: 10.1111/ctr.12259. Epub 2013 Oct 9.

PubMed [citation]
PMID:
24118554
See all PubMed Citations (10)

Details of each submission

From Counsyl, SCV000789962.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001235665.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change replaces valine with phenylalanine at codon 1262 of the ATP7B protein (p.Val1262Phe). The valine residue is highly conserved and there is a small physicochemical difference between valine and phenylalanine. This variant is present in population databases (rs769484789, ExAC 0.009%). This variant has been observed in individual(s) affected with Wilson's disease (PMID: PMID: 10544227, 20485189, Invitae). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 550902). This variant has been reported to affect ATP7B protein function (PMID: 19937698). For these reasons, this variant has been classified as Pathogenic.

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

From Nilou-Genome Lab, SCV001977234.1

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

Last Updated: Nov 27, 2021

Support Center