NM_000053.4(ATP7B):c.3226A>G (p.Thr1076Ala) AND Wilson disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 26, 2023
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:: RCV004011962.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.3226A>G (p.Thr1076Ala)]

NM_000053.4(ATP7B):c.3226A>G (p.Thr1076Ala)

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.3226A>G (p.Thr1076Ala)

HGVS:

NC_000013.11:g.51944126T>C
NG_008806.1:g.72369A>G
NM_000053.4:c.3226A>GMANE SELECT
NM_001005918.3:c.2605A>G
NM_001243182.2:c.2893A>G
NM_001330578.2:c.2992A>G
NM_001330579.2:c.2974A>G
NM_001406511.1:c.3226A>G
NM_001406512.1:c.3226A>G
NM_001406513.1:c.3220A>G
NM_001406514.1:c.3193A>G
NM_001406515.1:c.3172A>G
NM_001406516.1:c.3172A>G
NM_001406517.1:c.3130A>G
NM_001406518.1:c.3130A>G
NM_001406519.1:c.3091A>G
NM_001406520.1:c.3082A>G
NM_001406521.1:c.3082A>G
NM_001406522.1:c.3082A>G
NM_001406523.1:c.3061-1572A>G
NM_001406524.1:c.3049A>G
NM_001406525.1:c.3031A>G
NM_001406526.1:c.3226A>G
NM_001406527.1:c.2992A>G
NM_001406528.1:c.2992A>G
NM_001406530.1:c.2986A>G
NM_001406531.1:c.2974A>G
NM_001406532.1:c.2974A>G
NM_001406534.1:c.2938A>G
NM_001406535.1:c.2896A>G
NM_001406536.1:c.2896A>G
NM_001406537.1:c.2887A>G
NM_001406538.1:c.2992A>G
NM_001406539.1:c.2797A>G
NM_001406540.1:c.2779A>G
NM_001406541.1:c.2740A>G
NM_001406542.1:c.2740A>G
NM_001406543.1:c.2878A>G
NM_001406544.1:c.2644A>G
NM_001406545.1:c.2578A>G
NM_001406546.1:c.2545A>G
NM_001406547.1:c.2383A>G
NM_001406548.1:c.1936A>G
NP_000044.2:p.Thr1076Ala
NP_001005918.1:p.Thr869Ala
NP_001230111.1:p.Thr965Ala
NP_001317507.1:p.Thr998Ala
NP_001317508.1:p.Thr992Ala
NP_001393440.1:p.Thr1076Ala
NP_001393441.1:p.Thr1076Ala
NP_001393442.1:p.Thr1074Ala
NP_001393443.1:p.Thr1065Ala
NP_001393444.1:p.Thr1058Ala
NP_001393445.1:p.Thr1058Ala
NP_001393446.1:p.Thr1044Ala
NP_001393447.1:p.Thr1044Ala
NP_001393448.1:p.Thr1031Ala
NP_001393449.1:p.Thr1028Ala
NP_001393450.1:p.Thr1028Ala
NP_001393451.1:p.Thr1028Ala
NP_001393453.1:p.Thr1017Ala
NP_001393454.1:p.Thr1011Ala
NP_001393455.1:p.Thr1076Ala
NP_001393456.1:p.Thr998Ala
NP_001393457.1:p.Thr998Ala
NP_001393459.1:p.Thr996Ala
NP_001393460.1:p.Thr992Ala
NP_001393461.1:p.Thr992Ala
NP_001393463.1:p.Thr980Ala
NP_001393464.1:p.Thr966Ala
NP_001393465.1:p.Thr966Ala
NP_001393466.1:p.Thr963Ala
NP_001393467.1:p.Thr998Ala
NP_001393468.1:p.Thr933Ala
NP_001393469.1:p.Thr927Ala
NP_001393470.1:p.Thr914Ala
NP_001393471.1:p.Thr914Ala
NP_001393472.1:p.Thr960Ala
NP_001393473.1:p.Thr882Ala
NP_001393474.1:p.Thr860Ala
NP_001393475.1:p.Thr849Ala
NP_001393476.1:p.Thr795Ala
NP_001393477.1:p.Thr646Ala
NC_000013.10:g.52518262T>C

Protein change:

T1011A

Molecular consequence:

NM_001406523.1:c.3061-1572A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000053.4:c.3226A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.2605A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2893A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2992A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2974A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406511.1:c.3226A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406512.1:c.3226A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406513.1:c.3220A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406514.1:c.3193A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406515.1:c.3172A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406516.1:c.3172A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406517.1:c.3130A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406518.1:c.3130A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406519.1:c.3091A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406520.1:c.3082A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406521.1:c.3082A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406522.1:c.3082A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406524.1:c.3049A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406525.1:c.3031A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406526.1:c.3226A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406527.1:c.2992A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406528.1:c.2992A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406530.1:c.2986A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406531.1:c.2974A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406532.1:c.2974A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406534.1:c.2938A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406535.1:c.2896A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406536.1:c.2896A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406537.1:c.2887A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406538.1:c.2992A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406539.1:c.2797A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406540.1:c.2779A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406541.1:c.2740A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406542.1:c.2740A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406543.1:c.2878A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406544.1:c.2644A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406545.1:c.2578A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406546.1:c.2545A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406547.1:c.2383A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406548.1:c.1936A>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

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1721078[uid] (1)
Taxonomy
PREDICTED: Homo sapiens nucleolar protein 9 (NOL9), transcript variant X1, mRNA
PREDICTED: Homo sapiens nucleolar protein 9 (NOL9), transcript variant X1, mRNA
gi|2217270897|ref|XM_005263493.5|

Nucleotide
Locally Advanced High Grade Sarcoma
Locally Advanced High Grade Sarcoma

MedGen
Locally Advanced Gastric Adenocarcinoma
Locally Advanced Gastric Adenocarcinoma

MedGen
Locally Advanced Prostate Neuroendocrine Carcinoma
Locally Advanced Prostate Neuroendocrine Carcinoma

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004831527	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Jun 26, 2023)	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

SCV004831527

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Jun 26, 2023)

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, SCV004831527.1

#	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 alanine at codon 1076 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 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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