NM_000053.4(ATP7B):c.1142T>G (p.Ile381Ser) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 20, 2014
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:: RCV002456483.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.1142T>G (p.Ile381Ser)]

NM_000053.4(ATP7B):c.1142T>G (p.Ile381Ser)

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.1142T>G (p.Ile381Ser)

HGVS:

NC_000013.11:g.51974078A>C
NG_008806.1:g.42417T>G
NM_000053.4:c.1142T>GMANE SELECT
NM_001005918.3:c.1142T>G
NM_001243182.2:c.809T>G
NM_001330578.2:c.1142T>G
NM_001330579.2:c.1142T>G
NP_000044.2:p.Ile381Ser
NP_001005918.1:p.Ile381Ser
NP_001230111.1:p.Ile270Ser
NP_001317507.1:p.Ile381Ser
NP_001317508.1:p.Ile381Ser
NC_000013.10:g.52548214A>C
NM_000053.3:c.1142T>G

Protein change:

I270S

Links:

dbSNP: rs766943890

NCBI 1000 Genomes Browser:

rs766943890

Molecular consequence:

NM_000053.4:c.1142T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.1142T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.809T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.1142T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.1142T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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polycomb protein SCMH1 isoform c [Homo sapiens]
polycomb protein SCMH1 isoform c [Homo sapiens]
gi|288557331|ref|NP_001165689.1|

Protein
Sprr2d small proline-rich protein 2D [Mus musculus]
Sprr2d small proline-rich protein 2D [Mus musculus]
Gene ID:20758

Gene
20758[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002613929	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 20, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002613929

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 20, 2014)

germline

clinical testing

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

Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A genetic study of Wilson's disease in the United Kingdom.

Coffey AJ, Durkie M, Hague S, McLay K, Emmerson J, Lo C, Klaffke S, Joyce CJ, Dhawan A, Hadzic N, Mieli-Vergani G, Kirk R, Elizabeth Allen K, Nicholl D, Wong S, Griffiths W, Smithson S, Giffin N, Taha A, Connolly S, Gillett GT, Tanner S, et al.

Brain. 2013 May;136(Pt 5):1476-87. doi: 10.1093/brain/awt035. Epub 2013 Mar 21.

PubMed [citation]

PMID:: 23518715
PMCID:: PMC3634195

Details of each submission

From Ambry Genetics, SCV002613929.2

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

Description

The p.I381S variant (also known as c.1142T>G), located in coding exon 2 of the ATP7B gene, results from a T to G substitution at nucleotide position 1142. The isoleucine at codon 381 is replaced by serine, an amino acid with dissimilar properties. In one study, this variant was confirmed to be in cis with a second variant, p.I1184T, and in trans with a pathogenic mutation in an individual with a clinical diagnosis of Wilson disease. In another patient in this study, this variant was also seen with p.I1184T as well as a different alteration; however phase was not determined (Coffey AJ, et al. Brain 2013 May; 136(Pt 5):1476-87). This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP) and 1000 Genomes Project. In the ESP, this variant was not observed in 6226 samples (12452 alleles) with coverage at this position. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence to date, the clinical significance of the p.I381S variant remains unclear.

#	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: May 1, 2024

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