NM_000053.4(ATP7B):c.727_728insA (p.Phe243fs) 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:: RCV004555804.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.727_728insA (p.Phe243fs)]

NM_000053.4(ATP7B):c.727_728insA (p.Phe243fs)

Gene:

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

Variant type:

Insertion

Cytogenetic location:

13q14.3

Genomic location:

Preferred name:

NM_000053.4(ATP7B):c.727_728insA (p.Phe243fs)

HGVS:

NC_000013.11:g.51974492_51974493insT
NG_008806.1:g.42002_42003insA
NM_000053.4:c.727_728insAMANE SELECT
NM_001005918.3:c.727_728insA
NM_001243182.2:c.727_728insA
NM_001330578.2:c.727_728insA
NM_001330579.2:c.727_728insA
NM_001406511.1:c.727_728insA
NM_001406512.1:c.727_728insA
NM_001406513.1:c.727_728insA
NM_001406514.1:c.727_728insA
NM_001406515.1:c.727_728insA
NM_001406516.1:c.727_728insA
NM_001406517.1:c.631_632insA
NM_001406518.1:c.631_632insA
NM_001406519.1:c.727_728insA
NM_001406520.1:c.727_728insA
NM_001406521.1:c.727_728insA
NM_001406522.1:c.727_728insA
NM_001406523.1:c.727_728insA
NM_001406524.1:c.727_728insA
NM_001406525.1:c.727_728insA
NM_001406526.1:c.727_728insA
NM_001406527.1:c.727_728insA
NM_001406528.1:c.727_728insA
NM_001406530.1:c.631_632insA
NM_001406531.1:c.727_728insA
NM_001406532.1:c.727_728insA
NM_001406534.1:c.727_728insA
NM_001406535.1:c.727_728insA
NM_001406536.1:c.631_632insA
NM_001406537.1:c.727_728insA
NM_001406538.1:c.727_728insA
NM_001406539.1:c.631_632insA
NM_001406540.1:c.727_728insA
NM_001406541.1:c.727_728insA
NM_001406542.1:c.727_728insA
NM_001406543.1:c.631_632insA
NM_001406544.1:c.631_632insA
NM_001406545.1:c.727_728insA
NM_001406546.1:c.727_728insA
NM_001406547.1:c.727_728insA
NM_001406548.1:c.727_728insA
NP_000044.2:p.Phe243fs
NP_001005918.1:p.Phe243fs
NP_001230111.1:p.Phe243fs
NP_001317507.1:p.Phe243fs
NP_001317508.1:p.Phe243fs
NP_001393440.1:p.Phe243fs
NP_001393441.1:p.Phe243fs
NP_001393442.1:p.Phe243fs
NP_001393443.1:p.Phe243fs
NP_001393444.1:p.Phe243fs
NP_001393445.1:p.Phe243fs
NP_001393446.1:p.Phe211fs
NP_001393447.1:p.Phe211fs
NP_001393448.1:p.Phe243fs
NP_001393449.1:p.Phe243fs
NP_001393450.1:p.Phe243fs
NP_001393451.1:p.Phe243fs
NP_001393452.1:p.Phe243fs
NP_001393453.1:p.Phe243fs
NP_001393454.1:p.Phe243fs
NP_001393455.1:p.Phe243fs
NP_001393456.1:p.Phe243fs
NP_001393457.1:p.Phe243fs
NP_001393459.1:p.Phe211fs
NP_001393460.1:p.Phe243fs
NP_001393461.1:p.Phe243fs
NP_001393463.1:p.Phe243fs
NP_001393464.1:p.Phe243fs
NP_001393465.1:p.Phe211fs
NP_001393466.1:p.Phe243fs
NP_001393467.1:p.Phe243fs
NP_001393468.1:p.Phe211fs
NP_001393469.1:p.Phe243fs
NP_001393470.1:p.Phe243fs
NP_001393471.1:p.Phe243fs
NP_001393472.1:p.Phe211fs
NP_001393473.1:p.Phe211fs
NP_001393474.1:p.Phe243fs
NP_001393475.1:p.Phe243fs
NP_001393476.1:p.Phe243fs
NP_001393477.1:p.Phe243fs
NC_000013.10:g.52548628_52548629insT

Protein change:

F211fs

Molecular consequence:

NM_000053.4:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001005918.3:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243182.2:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330578.2:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330579.2:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406511.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406512.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406513.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406514.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406515.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406516.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406517.1:c.631_632insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406518.1:c.631_632insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406519.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406520.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406521.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406522.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406523.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406524.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406525.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406526.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406527.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406528.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406530.1:c.631_632insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406531.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406532.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406534.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406535.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406536.1:c.631_632insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406537.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406538.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406539.1:c.631_632insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406540.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406541.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406542.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406543.1:c.631_632insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406544.1:c.631_632insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406545.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406546.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406547.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406548.1:c.727_728insA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Homo sapiens poly(ADP-ribose) polymerase family member 12 (PARP12), transcript v...
Homo sapiens poly(ADP-ribose) polymerase family member 12 (PARP12), transcript variant 1, mRNA
gi|733214993|ref|NM_022750.3|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005044812	Neuberg Centre For Genomic Medicine, NCGM	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

SCV005044812

Neuberg Centre For Genomic Medicine, NCGM

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
not provided	germline	yes	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 Neuberg Centre For Genomic Medicine, NCGM, SCV005044812.2

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

Description

The frameshift c.727_728insA p.Phe243TyrfsTer2 variant in the ATP7B gene gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant causes a frameshift starting with codon Phenylalanine 243, changes this amino acid to Tyrosine residue, and creates a premature Stop codon at position 2 of the new reading frame, denoted p.Phe243TyrfsTer2. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

#	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		not provided	not provided	not provided	not provided

Last Updated: Jun 17, 2024

ClinVar

Relating variation to medicine