NM_000053.4(ATP7B):c.3550dup (p.Ile1184fs) AND Wilson disease

Germline classification:: Likely pathogenic (1 submission)
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:: RCV003227575.1

Allele description [Variation Report for NM_000053.4(ATP7B):c.3550dup (p.Ile1184fs)]

NM_000053.4(ATP7B):c.3550dup (p.Ile1184fs)

Gene:

ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

13q14.3

Genomic location:

Preferred name:

NM_000053.4(ATP7B):c.3550dup (p.Ile1184fs)

HGVS:

NC_000013.11:g.51941087dup
NG_008806.1:g.75408dup
NM_000053.4:c.3550dupMANE SELECT
NM_001005918.3:c.2929dup
NM_001243182.2:c.3217dup
NM_001330578.2:c.3316dup
NM_001330579.2:c.3298dup
NM_001406511.1:c.3550dup
NM_001406512.1:c.3550dup
NM_001406513.1:c.3544dup
NM_001406514.1:c.3517dup
NM_001406515.1:c.3496dup
NM_001406516.1:c.3496dup
NM_001406517.1:c.3454dup
NM_001406518.1:c.3454dup
NM_001406519.1:c.3415dup
NM_001406520.1:c.3406dup
NM_001406521.1:c.3406dup
NM_001406522.1:c.3406dup
NM_001406523.1:c.3367dup
NM_001406524.1:c.3373dup
NM_001406525.1:c.3355dup
NM_001406526.1:c.3550dup
NM_001406527.1:c.3316dup
NM_001406528.1:c.3316dup
NM_001406530.1:c.3310dup
NM_001406531.1:c.3298dup
NM_001406532.1:c.3298dup
NM_001406534.1:c.3262dup
NM_001406535.1:c.3220dup
NM_001406536.1:c.3220dup
NM_001406537.1:c.3211dup
NM_001406538.1:c.3178+1299dup
NM_001406539.1:c.3121dup
NM_001406540.1:c.3103dup
NM_001406541.1:c.3064dup
NM_001406542.1:c.3064dup
NM_001406543.1:c.3064+1299dup
NM_001406544.1:c.2968dup
NM_001406545.1:c.2902dup
NM_001406546.1:c.2869dup
NM_001406547.1:c.2707dup
NM_001406548.1:c.2260dup
NP_000044.2:p.Ile1184fs
NP_001005918.1:p.Ile977fs
NP_001230111.1:p.Ile1073fs
NP_001317507.1:p.Ile1106fs
NP_001317508.1:p.Ile1100fs
NP_001393440.1:p.Ile1184fs
NP_001393441.1:p.Ile1184fs
NP_001393442.1:p.Ile1182fs
NP_001393443.1:p.Ile1173fs
NP_001393444.1:p.Ile1166fs
NP_001393445.1:p.Ile1166fs
NP_001393446.1:p.Ile1152fs
NP_001393447.1:p.Ile1152fs
NP_001393448.1:p.Ile1139fs
NP_001393449.1:p.Ile1136fs
NP_001393450.1:p.Ile1136fs
NP_001393451.1:p.Ile1136fs
NP_001393452.1:p.Ile1123fs
NP_001393453.1:p.Ile1125fs
NP_001393454.1:p.Ile1119fs
NP_001393455.1:p.Ile1184fs
NP_001393456.1:p.Ile1106fs
NP_001393457.1:p.Ile1106fs
NP_001393459.1:p.Ile1104fs
NP_001393460.1:p.Ile1100fs
NP_001393461.1:p.Ile1100fs
NP_001393463.1:p.Ile1088fs
NP_001393464.1:p.Ile1074fs
NP_001393465.1:p.Ile1074fs
NP_001393466.1:p.Ile1071fs
NP_001393468.1:p.Ile1041fs
NP_001393469.1:p.Ile1035fs
NP_001393470.1:p.Ile1022fs
NP_001393471.1:p.Ile1022fs
NP_001393473.1:p.Ile990fs
NP_001393474.1:p.Ile968fs
NP_001393475.1:p.Ile957fs
NP_001393476.1:p.Ile903fs
NP_001393477.1:p.Ile754fs
NC_000013.10:g.52515223dup
NM_000053.4:c.3550dupAMANE SELECT

Protein change:

I1022fs

Molecular consequence:

NM_000053.4:c.3550dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001005918.3:c.2929dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243182.2:c.3217dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330578.2:c.3316dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330579.2:c.3298dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406511.1:c.3550dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406512.1:c.3550dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406513.1:c.3544dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406514.1:c.3517dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406515.1:c.3496dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406516.1:c.3496dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406517.1:c.3454dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406518.1:c.3454dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406519.1:c.3415dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406520.1:c.3406dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406521.1:c.3406dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406522.1:c.3406dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406523.1:c.3367dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406524.1:c.3373dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406525.1:c.3355dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406526.1:c.3550dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406527.1:c.3316dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406528.1:c.3316dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406530.1:c.3310dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406531.1:c.3298dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406532.1:c.3298dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406534.1:c.3262dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406535.1:c.3220dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406536.1:c.3220dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406537.1:c.3211dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406539.1:c.3121dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406540.1:c.3103dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406541.1:c.3064dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406542.1:c.3064dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406544.1:c.2968dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406545.1:c.2902dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406546.1:c.2869dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406547.1:c.2707dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406548.1:c.2260dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406538.1:c.3178+1299dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001406543.1:c.3064+1299dup - intron variant - [Sequence Ontology: SO:0001627]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003924057	Lifecell International Pvt. Ltd	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	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

SCV003924057

Lifecell International Pvt. Ltd

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

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
Asian	germline	yes	1	not provided	not provided	not provided	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 Lifecell International Pvt. Ltd, SCV003924057.1

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

Description

A Heterozygous Frameshift variant c.3550dupA in Exon 16 of the ATP7B gene that results in the amino acid substitution p.Ile1184fs*2 was identified. The observed variant novel in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. Based on the above evidence this variant has been classified as Likely Pathogenic according to the ACMG guidelines.

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

Last Updated: May 27, 2023

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