NM_000053.4(ATP7B):c.2681C>G (p.Thr894Ser) AND Wilson disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 5, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004016982.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.2681C>G (p.Thr894Ser)]

NM_000053.4(ATP7B):c.2681C>G (p.Thr894Ser)

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.2681C>G (p.Thr894Ser)

HGVS:

NC_000013.11:g.51950056G>C
NG_008806.1:g.66439C>G
NM_000053.4:c.2681C>GMANE SELECT
NM_001005918.3:c.2195C>G
NM_001243182.2:c.2348C>G
NM_001330578.2:c.2447C>G
NM_001330579.2:c.2429C>G
NM_001406511.1:c.2681C>G
NM_001406512.1:c.2681C>G
NM_001406513.1:c.2681C>G
NM_001406514.1:c.2648C>G
NM_001406515.1:c.2681C>G
NM_001406516.1:c.2681C>G
NM_001406517.1:c.2585C>G
NM_001406518.1:c.2585C>G
NM_001406519.1:c.2681C>G
NM_001406520.1:c.2537C>G
NM_001406521.1:c.2537C>G
NM_001406522.1:c.2537C>G
NM_001406523.1:c.2681C>G
NM_001406524.1:c.2504C>G
NM_001406525.1:c.2681C>G
NM_001406526.1:c.2681C>G
NM_001406527.1:c.2447C>G
NM_001406528.1:c.2447C>G
NM_001406530.1:c.2441C>G
NM_001406531.1:c.2429C>G
NM_001406532.1:c.2429C>G
NM_001406534.1:c.2447C>G
NM_001406535.1:c.2681C>G
NM_001406536.1:c.2351C>G
NM_001406537.1:c.2537C>G
NM_001406538.1:c.2447C>G
NM_001406539.1:c.2252C>G
NM_001406540.1:c.2429C>G
NM_001406541.1:c.2195C>G
NM_001406542.1:c.2195C>G
NM_001406543.1:c.2333C>G
NM_001406544.1:c.2099C>G
NM_001406545.1:c.2033C>G
NM_001406546.1:c.2195C>G
NM_001406547.1:c.2033C>G
NM_001406548.1:c.1391C>G
NP_000044.2:p.Thr894Ser
NP_001005918.1:p.Thr732Ser
NP_001230111.1:p.Thr783Ser
NP_001317507.1:p.Thr816Ser
NP_001317508.1:p.Thr810Ser
NP_001393440.1:p.Thr894Ser
NP_001393441.1:p.Thr894Ser
NP_001393442.1:p.Thr894Ser
NP_001393443.1:p.Thr883Ser
NP_001393444.1:p.Thr894Ser
NP_001393445.1:p.Thr894Ser
NP_001393446.1:p.Thr862Ser
NP_001393447.1:p.Thr862Ser
NP_001393448.1:p.Thr894Ser
NP_001393449.1:p.Thr846Ser
NP_001393450.1:p.Thr846Ser
NP_001393451.1:p.Thr846Ser
NP_001393452.1:p.Thr894Ser
NP_001393453.1:p.Thr835Ser
NP_001393454.1:p.Thr894Ser
NP_001393455.1:p.Thr894Ser
NP_001393456.1:p.Thr816Ser
NP_001393457.1:p.Thr816Ser
NP_001393459.1:p.Thr814Ser
NP_001393460.1:p.Thr810Ser
NP_001393461.1:p.Thr810Ser
NP_001393463.1:p.Thr816Ser
NP_001393464.1:p.Thr894Ser
NP_001393465.1:p.Thr784Ser
NP_001393466.1:p.Thr846Ser
NP_001393467.1:p.Thr816Ser
NP_001393468.1:p.Thr751Ser
NP_001393469.1:p.Thr810Ser
NP_001393470.1:p.Thr732Ser
NP_001393471.1:p.Thr732Ser
NP_001393472.1:p.Thr778Ser
NP_001393473.1:p.Thr700Ser
NP_001393474.1:p.Thr678Ser
NP_001393475.1:p.Thr732Ser
NP_001393476.1:p.Thr678Ser
NP_001393477.1:p.Thr464Ser
NC_000013.10:g.52524192G>C

Protein change:

T464S

Molecular consequence:

NM_000053.4:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.2195C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2348C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2447C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2429C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406511.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406512.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406513.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406514.1:c.2648C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406515.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406516.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406517.1:c.2585C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406518.1:c.2585C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406519.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406520.1:c.2537C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406521.1:c.2537C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406522.1:c.2537C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406523.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406524.1:c.2504C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406525.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406526.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406527.1:c.2447C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406528.1:c.2447C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406530.1:c.2441C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406531.1:c.2429C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406532.1:c.2429C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406534.1:c.2447C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406535.1:c.2681C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406536.1:c.2351C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406537.1:c.2537C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406538.1:c.2447C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406539.1:c.2252C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406540.1:c.2429C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406541.1:c.2195C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406542.1:c.2195C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406543.1:c.2333C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406544.1:c.2099C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406545.1:c.2033C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406546.1:c.2195C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406547.1:c.2033C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406548.1:c.1391C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

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

Recent activity

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H.sapiens mRNA for 218kD Mi-2 protein
H.sapiens mRNA for 218kD Mi-2 protein
gi|1107695|emb|X86691.1|

Nucleotide
CHC2 zinc finger domain-containing protein [Candidatus Nardonella dryophthoridic...
CHC2 zinc finger domain-containing protein [Candidatus Nardonella dryophthoridicola]
gi|2250027524|ref|WP_250672645.1|

Protein
IS256-like element IS3503 family transposase [Corynebacterium urealyticum]
IS256-like element IS3503 family transposase [Corynebacterium urealyticum]
gi|501328924|ref|WP_012360559.1|

Protein
Rattus norvegicus DLG associated protein 3 (Dlgap3), transcript variant 1, mRNA
Rattus norvegicus DLG associated protein 3 (Dlgap3), transcript variant 1, mRNA
gi|2075472653|ref|NM_173138.6|

Nucleotide
disks large-associated protein 3 isoform 1 [Rattus norvegicus]
disks large-associated protein 3 isoform 1 [Rattus norvegicus]
gi|443906724|ref|NP_775161.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004842777	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Feb 5, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004842777

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Feb 5, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	108544	not provided	clinical 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 All of Us Research Program, National Institutes of Health, SCV004842777.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

This missense variant replaces threonine with serine at codon 894 of the ATP7B protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, 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 not been identified 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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