NM_000053.4(ATP7B):c.1028C>G (p.Ser343Cys) AND Wilson disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 24, 2022
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:: RCV002972669.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.1028C>G (p.Ser343Cys)]

NM_000053.4(ATP7B):c.1028C>G (p.Ser343Cys)

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.1028C>G (p.Ser343Cys)

HGVS:

NC_000013.11:g.51974192G>C
NG_008806.1:g.42303C>G
NM_000053.4:c.1028C>GMANE SELECT
NM_001005918.3:c.1028C>G
NM_001243182.2:c.803-108C>G
NM_001330578.2:c.1028C>G
NM_001330579.2:c.1028C>G
NM_001406511.1:c.1028C>G
NM_001406512.1:c.1028C>G
NM_001406513.1:c.1028C>G
NM_001406514.1:c.1028C>G
NM_001406515.1:c.1028C>G
NM_001406516.1:c.1028C>G
NM_001406517.1:c.932C>G
NM_001406518.1:c.932C>G
NM_001406519.1:c.1028C>G
NM_001406520.1:c.1028C>G
NM_001406521.1:c.1028C>G
NM_001406522.1:c.1028C>G
NM_001406523.1:c.1028C>G
NM_001406524.1:c.1028C>G
NM_001406525.1:c.1028C>G
NM_001406526.1:c.1028C>G
NM_001406527.1:c.1028C>G
NM_001406528.1:c.1028C>G
NM_001406530.1:c.932C>G
NM_001406531.1:c.1028C>G
NM_001406532.1:c.1028C>G
NM_001406534.1:c.1028C>G
NM_001406535.1:c.1028C>G
NM_001406536.1:c.932C>G
NM_001406537.1:c.1028C>G
NM_001406538.1:c.1028C>G
NM_001406540.1:c.1028C>G
NM_001406541.1:c.1028C>G
NM_001406542.1:c.1028C>G
NM_001406543.1:c.932C>G
NM_001406544.1:c.932C>G
NM_001406545.1:c.1028C>G
NM_001406546.1:c.1028C>G
NM_001406547.1:c.1028C>G
NM_001406548.1:c.1028C>G
NP_000044.2:p.Ser343Cys
NP_001005918.1:p.Ser343Cys
NP_001317507.1:p.Ser343Cys
NP_001317508.1:p.Ser343Cys
NP_001393440.1:p.Ser343Cys
NP_001393441.1:p.Ser343Cys
NP_001393442.1:p.Ser343Cys
NP_001393443.1:p.Ser343Cys
NP_001393444.1:p.Ser343Cys
NP_001393445.1:p.Ser343Cys
NP_001393446.1:p.Ser311Cys
NP_001393447.1:p.Ser311Cys
NP_001393448.1:p.Ser343Cys
NP_001393449.1:p.Ser343Cys
NP_001393450.1:p.Ser343Cys
NP_001393451.1:p.Ser343Cys
NP_001393452.1:p.Ser343Cys
NP_001393453.1:p.Ser343Cys
NP_001393454.1:p.Ser343Cys
NP_001393455.1:p.Ser343Cys
NP_001393456.1:p.Ser343Cys
NP_001393457.1:p.Ser343Cys
NP_001393459.1:p.Ser311Cys
NP_001393460.1:p.Ser343Cys
NP_001393461.1:p.Ser343Cys
NP_001393463.1:p.Ser343Cys
NP_001393464.1:p.Ser343Cys
NP_001393465.1:p.Ser311Cys
NP_001393466.1:p.Ser343Cys
NP_001393467.1:p.Ser343Cys
NP_001393469.1:p.Ser343Cys
NP_001393470.1:p.Ser343Cys
NP_001393471.1:p.Ser343Cys
NP_001393472.1:p.Ser311Cys
NP_001393473.1:p.Ser311Cys
NP_001393474.1:p.Ser343Cys
NP_001393475.1:p.Ser343Cys
NP_001393476.1:p.Ser343Cys
NP_001393477.1:p.Ser343Cys
NC_000013.10:g.52548328G>C

Protein change:

S311C

Molecular consequence:

NM_001243182.2:c.803-108C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000053.4:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406511.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406512.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406513.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406514.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406515.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406516.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406517.1:c.932C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406518.1:c.932C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406519.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406520.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406521.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406522.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406523.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406524.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406525.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406526.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406527.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406528.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406530.1:c.932C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406531.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406532.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406534.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406535.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406536.1:c.932C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406537.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406538.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406540.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406541.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406542.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406543.1:c.932C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406544.1:c.932C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406545.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406546.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406547.1:c.1028C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406548.1:c.1028C>G - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003292454	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 24, 2022)	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

SCV003292454

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 24, 2022)

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	not provided	not provided	not provided	not provided	not provided	clinical 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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003292454.1

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

Description

This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 343 of the ATP7B protein (p.Ser343Cys). 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. 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.

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

Last Updated: Sep 29, 2024

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