NM_000053.4(ATP7B):c.3543_3551delinsTCTGC (p.Val1182fs) AND Wilson disease

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 28, 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:: RCV003464960.1

Allele description [Variation Report for NM_000053.4(ATP7B):c.3543_3551delinsTCTGC (p.Val1182fs)]

NM_000053.4(ATP7B):c.3543_3551delinsTCTGC (p.Val1182fs)

Gene:

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

Variant type:

Indel

Cytogenetic location:

13q14.3

Genomic location:

Preferred name:

NM_000053.4(ATP7B):c.3543_3551delinsTCTGC (p.Val1182fs)

HGVS:

NC_000013.11:g.51941086_51941094delinsGCAGA
NG_008806.1:g.75401_75409delinsTCTGC
NM_000053.4:c.3543_3551delinsTCTGCMANE SELECT
NM_001005918.3:c.2922_2930delinsTCTGC
NM_001243182.2:c.3210_3218delinsTCTGC
NM_001330578.2:c.3309_3317delinsTCTGC
NM_001330579.2:c.3291_3299delinsTCTGC
NM_001406511.1:c.3543_3551delinsTCTGC
NM_001406512.1:c.3543_3551delinsTCTGC
NM_001406513.1:c.3537_3545delinsTCTGC
NM_001406514.1:c.3510_3518delinsTCTGC
NM_001406515.1:c.3489_3497delinsTCTGC
NM_001406516.1:c.3489_3497delinsTCTGC
NM_001406517.1:c.3447_3455delinsTCTGC
NM_001406518.1:c.3447_3455delinsTCTGC
NM_001406519.1:c.3408_3416delinsTCTGC
NM_001406520.1:c.3399_3407delinsTCTGC
NM_001406521.1:c.3399_3407delinsTCTGC
NM_001406522.1:c.3399_3407delinsTCTGC
NM_001406523.1:c.3360_3368delinsTCTGC
NM_001406524.1:c.3366_3374delinsTCTGC
NM_001406525.1:c.3348_3356delinsTCTGC
NM_001406526.1:c.3543_3551delinsTCTGC
NM_001406527.1:c.3309_3317delinsTCTGC
NM_001406528.1:c.3309_3317delinsTCTGC
NM_001406530.1:c.3303_3311delinsTCTGC
NM_001406531.1:c.3291_3299delinsTCTGC
NM_001406532.1:c.3291_3299delinsTCTGC
NM_001406534.1:c.3255_3263delinsTCTGC
NM_001406535.1:c.3213_3221delinsTCTGC
NM_001406536.1:c.3213_3221delinsTCTGC
NM_001406537.1:c.3204_3212delinsTCTGC
NM_001406538.1:c.3178+1292_3178+1300delinsTCTGC
NM_001406539.1:c.3114_3122delinsTCTGC
NM_001406540.1:c.3096_3104delinsTCTGC
NM_001406541.1:c.3057_3065delinsTCTGC
NM_001406542.1:c.3057_3065delinsTCTGC
NM_001406543.1:c.3064+1292_3064+1300delinsTCTGC
NM_001406544.1:c.2961_2969delinsTCTGC
NM_001406545.1:c.2895_2903delinsTCTGC
NM_001406546.1:c.2862_2870delinsTCTGC
NM_001406547.1:c.2700_2708delinsTCTGC
NM_001406548.1:c.2253_2261delinsTCTGC
NP_000044.2:p.Val1182fs
NP_001005918.1:p.Val975fs
NP_001230111.1:p.Val1071fs
NP_001317507.1:p.Val1104fs
NP_001317508.1:p.Val1098fs
NP_001393440.1:p.Val1182fs
NP_001393441.1:p.Val1182fs
NP_001393442.1:p.Val1180fs
NP_001393443.1:p.Val1171fs
NP_001393444.1:p.Val1164fs
NP_001393445.1:p.Val1164fs
NP_001393446.1:p.Val1150fs
NP_001393447.1:p.Val1150fs
NP_001393448.1:p.Val1137fs
NP_001393449.1:p.Val1134fs
NP_001393450.1:p.Val1134fs
NP_001393451.1:p.Val1134fs
NP_001393452.1:p.Val1121fs
NP_001393453.1:p.Val1123fs
NP_001393454.1:p.Val1117fs
NP_001393455.1:p.Val1182fs
NP_001393456.1:p.Val1104fs
NP_001393457.1:p.Val1104fs
NP_001393459.1:p.Val1102fs
NP_001393460.1:p.Val1098fs
NP_001393461.1:p.Val1098fs
NP_001393463.1:p.Val1086fs
NP_001393464.1:p.Val1072fs
NP_001393465.1:p.Val1072fs
NP_001393466.1:p.Val1069fs
NP_001393468.1:p.Val1039fs
NP_001393469.1:p.Val1033fs
NP_001393470.1:p.Val1020fs
NP_001393471.1:p.Val1020fs
NP_001393473.1:p.Val988fs
NP_001393474.1:p.Val966fs
NP_001393475.1:p.Val955fs
NP_001393476.1:p.Val901fs
NP_001393477.1:p.Val752fs
NC_000013.10:g.52515222_52515230delinsGCAGA

Protein change:

V1020fs

Molecular consequence:

NM_000053.4:c.3543_3551delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001005918.3:c.2922_2930delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243182.2:c.3210_3218delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330578.2:c.3309_3317delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330579.2:c.3291_3299delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406511.1:c.3543_3551delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406512.1:c.3543_3551delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406513.1:c.3537_3545delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406514.1:c.3510_3518delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406515.1:c.3489_3497delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406516.1:c.3489_3497delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406517.1:c.3447_3455delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406518.1:c.3447_3455delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406519.1:c.3408_3416delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406520.1:c.3399_3407delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406521.1:c.3399_3407delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406522.1:c.3399_3407delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406523.1:c.3360_3368delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406524.1:c.3366_3374delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406525.1:c.3348_3356delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406526.1:c.3543_3551delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406527.1:c.3309_3317delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406528.1:c.3309_3317delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406530.1:c.3303_3311delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406531.1:c.3291_3299delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406532.1:c.3291_3299delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406534.1:c.3255_3263delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406535.1:c.3213_3221delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406536.1:c.3213_3221delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406537.1:c.3204_3212delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406539.1:c.3114_3122delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406540.1:c.3096_3104delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406541.1:c.3057_3065delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406542.1:c.3057_3065delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406544.1:c.2961_2969delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406545.1:c.2895_2903delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406546.1:c.2862_2870delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406547.1:c.2700_2708delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406548.1:c.2253_2261delinsTCTGC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406538.1:c.3178+1292_3178+1300delinsTCTGC - intron variant - [Sequence Ontology: SO:0001627]
NM_001406543.1:c.3064+1292_3064+1300delinsTCTGC - intron variant - [Sequence Ontology: SO:0001627]

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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PREDICTED: Xenopus laevis NGG1 interacting factor 3 like 1 S homeolog (nif3l1.S)...
PREDICTED: Xenopus laevis NGG1 interacting factor 3 like 1 S homeolog (nif3l1.S), transcript variant X1, mRNA
gi|2038324045|ref|XM_018237647.2|

Nucleotide
cytochrome oxidase subunit 1, partial (mitochondrion) [Planiliza affinis]
cytochrome oxidase subunit 1, partial (mitochondrion) [Planiliza affinis]
gi|2489543863|gb|WGF19430.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004216478	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 28, 2023)	unknown	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

SCV004216478

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 28, 2023)

unknown

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	unknown	unknown	not provided	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 Baylor Genetics, SCV004216478.1

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

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

Last Updated: Dec 30, 2023

ClinVar

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