NM_000053.4(ATP7B):c.2356-1G>C AND Wilson disease

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Dec 6, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000665943.4

Allele description [Variation Report for NM_000053.4(ATP7B):c.2356-1G>C]

NM_000053.4(ATP7B):c.2356-1G>C

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.2356-1G>C

HGVS:

NC_000013.11:g.51957608C>G
NG_008806.1:g.58887G>C
NM_000053.4:c.2356-1G>CMANE SELECT
NM_001005918.3:c.1870-1G>C
NM_001243182.2:c.2023-1G>C
NM_001330578.2:c.2122-1G>C
NM_001330579.2:c.2104-1G>C
NM_001406511.1:c.2356-1G>C
NM_001406512.1:c.2356-1G>C
NM_001406513.1:c.2356-1G>C
NM_001406514.1:c.2323-1G>C
NM_001406515.1:c.2356-1G>C
NM_001406516.1:c.2356-1G>C
NM_001406517.1:c.2260-1G>C
NM_001406518.1:c.2260-1G>C
NM_001406519.1:c.2356-1G>C
NM_001406520.1:c.2212-1G>C
NM_001406521.1:c.2212-1G>C
NM_001406522.1:c.2212-1G>C
NM_001406523.1:c.2356-1G>C
NM_001406524.1:c.2179-1G>C
NM_001406525.1:c.2356-1G>C
NM_001406526.1:c.2356-1G>C
NM_001406527.1:c.2122-1G>C
NM_001406528.1:c.2122-1G>C
NM_001406530.1:c.2116-1G>C
NM_001406531.1:c.2104-1G>C
NM_001406532.1:c.2104-1G>C
NM_001406534.1:c.2122-1G>C
NM_001406535.1:c.2356-1G>C
NM_001406536.1:c.2026-1G>C
NM_001406537.1:c.2212-1G>C
NM_001406538.1:c.2122-1G>C
NM_001406539.1:c.1927-1G>C
NM_001406540.1:c.2104-1G>C
NM_001406541.1:c.1870-1G>C
NM_001406542.1:c.1870-1G>C
NM_001406543.1:c.2008-1G>C
NM_001406544.1:c.1774-1G>C
NM_001406545.1:c.1708-1G>C
NM_001406546.1:c.1870-1G>C
NM_001406547.1:c.1708-1G>C
NM_001406548.1:c.1286-7447G>C
NC_000013.10:g.52531744C>G
NM_000053.3:c.2356-1G>C

Links:

dbSNP: rs1555290925

NCBI 1000 Genomes Browser:

rs1555290925

Molecular consequence:

NM_001406548.1:c.1286-7447G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000053.4:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001005918.3:c.1870-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001243182.2:c.2023-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001330578.2:c.2122-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001330579.2:c.2104-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406511.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406512.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406513.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406514.1:c.2323-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406515.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406516.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406517.1:c.2260-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406518.1:c.2260-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406519.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406520.1:c.2212-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406521.1:c.2212-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406522.1:c.2212-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406523.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406524.1:c.2179-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406525.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406526.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406527.1:c.2122-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406528.1:c.2122-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406530.1:c.2116-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406531.1:c.2104-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406532.1:c.2104-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406534.1:c.2122-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406535.1:c.2356-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406536.1:c.2026-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406537.1:c.2212-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406538.1:c.2122-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406539.1:c.1927-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406540.1:c.2104-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406541.1:c.1870-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406542.1:c.1870-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406543.1:c.2008-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406544.1:c.1774-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406545.1:c.1708-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406546.1:c.1870-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406547.1:c.1708-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV000790155	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Mar 14, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002303881	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Dec 6, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16199547, 10441329, 16283883, 27022412, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000790155

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Mar 14, 2017)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV002303881

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Dec 6, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Null mutation of the murine ATP7B (Wilson disease) gene results in intracellular copper accumulation and late-onset hepatic nodular transformation.

Buiakova OI, Xu J, Lutsenko S, Zeitlin S, Das K, Das S, Ross BM, Mekios C, Scheinberg IH, Gilliam TC.

Hum Mol Genet. 1999 Sep;8(9):1665-71.

PubMed [citation]

PMID:: 10441329

See all PubMed Citations (5)

Details of each submission

From Counsyl, SCV000790155.1

#	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

From Invitae, SCV002303881.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change affects an acceptor splice site in intron 8 of the ATP7B gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Wilson disease (PMID: 27022412). ClinVar contains an entry for this variant (Variation ID: 550995). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, 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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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