NM_000053.4(ATP7B):c.732del (p.Asn244fs) 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:: RCV004547243.1

Allele description [Variation Report for NM_000053.4(ATP7B):c.732del (p.Asn244fs)]

NM_000053.4(ATP7B):c.732del (p.Asn244fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

13q14.3

Genomic location:

Preferred name:

NM_000053.4(ATP7B):c.732del (p.Asn244fs)

HGVS:

NC_000013.11:g.51974488del
NG_008806.1:g.42007del
NM_000053.4:c.732delMANE SELECT
NM_001005918.3:c.732del
NM_001243182.2:c.732del
NM_001330578.2:c.732del
NM_001330579.2:c.732del
NM_001406511.1:c.732del
NM_001406512.1:c.732del
NM_001406513.1:c.732del
NM_001406514.1:c.732del
NM_001406515.1:c.732del
NM_001406516.1:c.732del
NM_001406517.1:c.636del
NM_001406518.1:c.636del
NM_001406519.1:c.732del
NM_001406520.1:c.732del
NM_001406521.1:c.732del
NM_001406522.1:c.732del
NM_001406523.1:c.732del
NM_001406524.1:c.732del
NM_001406525.1:c.732del
NM_001406526.1:c.732del
NM_001406527.1:c.732del
NM_001406528.1:c.732del
NM_001406530.1:c.636del
NM_001406531.1:c.732del
NM_001406532.1:c.732del
NM_001406534.1:c.732del
NM_001406535.1:c.732del
NM_001406536.1:c.636del
NM_001406537.1:c.732del
NM_001406538.1:c.732del
NM_001406539.1:c.636del
NM_001406540.1:c.732del
NM_001406541.1:c.732del
NM_001406542.1:c.732del
NM_001406543.1:c.636del
NM_001406544.1:c.636del
NM_001406545.1:c.732del
NM_001406546.1:c.732del
NM_001406547.1:c.732del
NM_001406548.1:c.732del
NP_000044.2:p.Asn244fs
NP_001005918.1:p.Asn244fs
NP_001230111.1:p.Asn244fs
NP_001317507.1:p.Asn244fs
NP_001317508.1:p.Asn244fs
NP_001393440.1:p.Asn244fs
NP_001393441.1:p.Asn244fs
NP_001393442.1:p.Asn244fs
NP_001393443.1:p.Asn244fs
NP_001393444.1:p.Asn244fs
NP_001393445.1:p.Asn244fs
NP_001393446.1:p.Asn212fs
NP_001393447.1:p.Asn212fs
NP_001393448.1:p.Asn244fs
NP_001393449.1:p.Asn244fs
NP_001393450.1:p.Asn244fs
NP_001393451.1:p.Asn244fs
NP_001393452.1:p.Asn244fs
NP_001393453.1:p.Asn244fs
NP_001393454.1:p.Asn244fs
NP_001393455.1:p.Asn244fs
NP_001393456.1:p.Asn244fs
NP_001393457.1:p.Asn244fs
NP_001393459.1:p.Asn212fs
NP_001393460.1:p.Asn244fs
NP_001393461.1:p.Asn244fs
NP_001393463.1:p.Asn244fs
NP_001393464.1:p.Asn244fs
NP_001393465.1:p.Asn212fs
NP_001393466.1:p.Asn244fs
NP_001393467.1:p.Asn244fs
NP_001393468.1:p.Asn212fs
NP_001393469.1:p.Asn244fs
NP_001393470.1:p.Asn244fs
NP_001393471.1:p.Asn244fs
NP_001393472.1:p.Asn212fs
NP_001393473.1:p.Asn212fs
NP_001393474.1:p.Asn244fs
NP_001393475.1:p.Asn244fs
NP_001393476.1:p.Asn244fs
NP_001393477.1:p.Asn244fs
NC_000013.10:g.52548624del

Protein change:

N212fs

Molecular consequence:

NM_000053.4:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001005918.3:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001243182.2:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330578.2:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330579.2:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406511.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406512.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406513.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406514.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406515.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406516.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406517.1:c.636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406518.1:c.636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406519.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406520.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406521.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406522.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406523.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406524.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406525.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406526.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406527.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406528.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406530.1:c.636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406531.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406532.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406534.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406535.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406536.1:c.636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406537.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406538.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406539.1:c.636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406540.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406541.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406542.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406543.1:c.636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406544.1:c.636del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406545.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406546.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406547.1:c.732del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406548.1:c.732del - 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

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Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 strain ATCC 13939 substr. R6...
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 strain ATCC 13939 substr. R6 chromosome I, complete sequence
gi|2124858180|ref|NZ_CP038991.1|

Nucleotide
Ancylomarina subtilis strain DSM 28825 Ga0310529_108, whole genome shotgun seque...
Ancylomarina subtilis strain DSM 28825 Ga0310529_108, whole genome shotgun sequence
gi|1577203881|gb|SHKN01000008.1||gn :SHKN01|Ga0310529_108

Nucleotide
PREDICTED: Rattus norvegicus surfactant protein B (Sftpb), transcript variant X1...
PREDICTED: Rattus norvegicus surfactant protein B (Sftpb), transcript variant X1, mRNA
gi|2678935877|ref|XM_006236657.5|

Nucleotide
Gm30392 predicted gene, 30392 [Mus musculus]
Gm30392 predicted gene, 30392 [Mus musculus]
Gene ID:102632266

Gene
Gm30392 AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005042640	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

SCV005042640

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, SCV005042640.1

#	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.732del p.Asn244LysfsTer18 variant in the ATP7B 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 Asparagine 244, changes this amino acid to Lysine residue, and creates a premature Stop codon at position 18 of the new reading frame, denoted p.Asn244LysfsTer18. 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: May 19, 2024

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