U.S. flag

An official website of the United States government

NM_000053.4(ATP7B):c.2674A>T (p.Asn892Tyr) AND Wilson disease

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
May 4, 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:
RCV002649576.4

Allele description [Variation Report for NM_000053.4(ATP7B):c.2674A>T (p.Asn892Tyr)]

NM_000053.4(ATP7B):c.2674A>T (p.Asn892Tyr)

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.2674A>T (p.Asn892Tyr)
HGVS:
  • NC_000013.11:g.51950063T>A
  • NG_008806.1:g.66432A>T
  • NM_000053.4:c.2674A>TMANE SELECT
  • NM_001005918.3:c.2188A>T
  • NM_001243182.2:c.2341A>T
  • NM_001330578.2:c.2440A>T
  • NM_001330579.2:c.2422A>T
  • NM_001406511.1:c.2674A>T
  • NM_001406512.1:c.2674A>T
  • NM_001406513.1:c.2674A>T
  • NM_001406514.1:c.2641A>T
  • NM_001406515.1:c.2674A>T
  • NM_001406516.1:c.2674A>T
  • NM_001406517.1:c.2578A>T
  • NM_001406518.1:c.2578A>T
  • NM_001406519.1:c.2674A>T
  • NM_001406520.1:c.2530A>T
  • NM_001406521.1:c.2530A>T
  • NM_001406522.1:c.2530A>T
  • NM_001406523.1:c.2674A>T
  • NM_001406524.1:c.2497A>T
  • NM_001406525.1:c.2674A>T
  • NM_001406526.1:c.2674A>T
  • NM_001406527.1:c.2440A>T
  • NM_001406528.1:c.2440A>T
  • NM_001406530.1:c.2434A>T
  • NM_001406531.1:c.2422A>T
  • NM_001406532.1:c.2422A>T
  • NM_001406534.1:c.2440A>T
  • NM_001406535.1:c.2674A>T
  • NM_001406536.1:c.2344A>T
  • NM_001406537.1:c.2530A>T
  • NM_001406538.1:c.2440A>T
  • NM_001406539.1:c.2245A>T
  • NM_001406540.1:c.2422A>T
  • NM_001406541.1:c.2188A>T
  • NM_001406542.1:c.2188A>T
  • NM_001406543.1:c.2326A>T
  • NM_001406544.1:c.2092A>T
  • NM_001406545.1:c.2026A>T
  • NM_001406546.1:c.2188A>T
  • NM_001406547.1:c.2026A>T
  • NM_001406548.1:c.1384A>T
  • NP_000044.2:p.Asn892Tyr
  • NP_001005918.1:p.Asn730Tyr
  • NP_001230111.1:p.Asn781Tyr
  • NP_001317507.1:p.Asn814Tyr
  • NP_001317508.1:p.Asn808Tyr
  • NP_001393440.1:p.Asn892Tyr
  • NP_001393441.1:p.Asn892Tyr
  • NP_001393442.1:p.Asn892Tyr
  • NP_001393443.1:p.Asn881Tyr
  • NP_001393444.1:p.Asn892Tyr
  • NP_001393445.1:p.Asn892Tyr
  • NP_001393446.1:p.Asn860Tyr
  • NP_001393447.1:p.Asn860Tyr
  • NP_001393448.1:p.Asn892Tyr
  • NP_001393449.1:p.Asn844Tyr
  • NP_001393450.1:p.Asn844Tyr
  • NP_001393451.1:p.Asn844Tyr
  • NP_001393452.1:p.Asn892Tyr
  • NP_001393453.1:p.Asn833Tyr
  • NP_001393454.1:p.Asn892Tyr
  • NP_001393455.1:p.Asn892Tyr
  • NP_001393456.1:p.Asn814Tyr
  • NP_001393457.1:p.Asn814Tyr
  • NP_001393459.1:p.Asn812Tyr
  • NP_001393460.1:p.Asn808Tyr
  • NP_001393461.1:p.Asn808Tyr
  • NP_001393463.1:p.Asn814Tyr
  • NP_001393464.1:p.Asn892Tyr
  • NP_001393465.1:p.Asn782Tyr
  • NP_001393466.1:p.Asn844Tyr
  • NP_001393467.1:p.Asn814Tyr
  • NP_001393468.1:p.Asn749Tyr
  • NP_001393469.1:p.Asn808Tyr
  • NP_001393470.1:p.Asn730Tyr
  • NP_001393471.1:p.Asn730Tyr
  • NP_001393472.1:p.Asn776Tyr
  • NP_001393473.1:p.Asn698Tyr
  • NP_001393474.1:p.Asn676Tyr
  • NP_001393475.1:p.Asn730Tyr
  • NP_001393476.1:p.Asn676Tyr
  • NP_001393477.1:p.Asn462Tyr
  • NC_000013.10:g.52524199T>A
Protein change:
N462Y
Molecular consequence:
  • NM_000053.4:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005918.3:c.2188A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243182.2:c.2341A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330578.2:c.2440A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330579.2:c.2422A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406511.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406512.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406513.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406514.1:c.2641A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406515.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406516.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406517.1:c.2578A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406518.1:c.2578A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406519.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406520.1:c.2530A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406521.1:c.2530A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406522.1:c.2530A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406523.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406524.1:c.2497A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406525.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406526.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406527.1:c.2440A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406528.1:c.2440A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406530.1:c.2434A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406531.1:c.2422A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406532.1:c.2422A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406534.1:c.2440A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406535.1:c.2674A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406536.1:c.2344A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406537.1:c.2530A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406538.1:c.2440A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406539.1:c.2245A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406540.1:c.2422A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406541.1:c.2188A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406542.1:c.2188A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406543.1:c.2326A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406544.1:c.2092A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406545.1:c.2026A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406546.1:c.2188A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406547.1:c.2026A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406548.1:c.1384A>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002973086Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 19, 2022) 		germlineclinical testing

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

SCV004824643All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain Significance
(May 4, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided108544not providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002973086.1

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

Description

This sequence change replaces asparagine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 892 of the ATP7B protein (p.Asn892Tyr). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with ATP7B-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ATP7B protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From All of Us Research Program, National Institutes of Health, SCV004824643.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

This missense variant replaces asparagine with tyrosine at codon 892 of the ATP7B protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with ATP7B-related disorders in the literature. This variant has been identified in 1/249586 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024