NM_000053.4(ATP7B):c.1158G>T (p.Gly386=) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 21, 2019
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:: RCV000779810.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.1158G>T (p.Gly386=)]

NM_000053.4(ATP7B):c.1158G>T (p.Gly386=)

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.1158G>T (p.Gly386=)

HGVS:

NC_000013.11:g.51974062C>A
NG_008806.1:g.42433G>T
NM_000053.4:c.1158G>TMANE SELECT
NM_001005918.3:c.1158G>T
NM_001243182.2:c.825G>T
NM_001330578.2:c.1158G>T
NM_001330579.2:c.1158G>T
NP_000044.2:p.Gly386=
NP_001005918.1:p.Gly386=
NP_001230111.1:p.Gly275=
NP_001317507.1:p.Gly386=
NP_001317508.1:p.Gly386=
NC_000013.10:g.52548198C>A
NM_000053.3:c.1158G>T

Links:

dbSNP: rs778775834

NCBI 1000 Genomes Browser:

rs778775834

Molecular consequence:

NM_000053.4:c.1158G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001005918.3:c.1158G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001243182.2:c.825G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330578.2:c.1158G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001330579.2:c.1158G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

Clear Turn Off Turn On

Insm1 insulinoma-associated 1 [Mus musculus]
Insm1 insulinoma-associated 1 [Mus musculus]
Gene ID:53626

Gene
53626[uid] AND (alive[prop]) (1)
Gene

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
SCV000916623	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Aug 21, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000916623

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Aug 21, 2019)

germline

clinical testing

Citation Link

Help

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000916623.2

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

Description

Variant summary: ATP7B c.1158G>T alters a non-conserved nucleotide resulting in a synonymous change. Several computational tools via ALAMUT predict a significant impact on normal splicing: Five predict the variant creates a cryptic exonic 5' donor site. One in-silico tool (TraP, Transcript-inferred Pathogenicity) predicts this synonymous variant to be possibly pathogenic (Gelfman_2017). However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.6e-05 in 249546 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1158G>T in individuals affected with Wilson Disease and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly benign.

#	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: Oct 20, 2024

ClinVar

Relating variation to medicine