NM_000053.4(ATP7B):c.1076G>A (p.Ser359Asn) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 21, 2023
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:: RCV003283409.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.1076G>A (p.Ser359Asn)]

NM_000053.4(ATP7B):c.1076G>A (p.Ser359Asn)

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.1076G>A (p.Ser359Asn)

HGVS:

NC_000013.11:g.51974144C>T
NG_008806.1:g.42351G>A
NM_000053.4:c.1076G>AMANE SELECT
NM_001005918.3:c.1076G>A
NM_001243182.2:c.803-60G>A
NM_001330578.2:c.1076G>A
NM_001330579.2:c.1076G>A
NM_001406511.1:c.1076G>A
NM_001406512.1:c.1076G>A
NM_001406513.1:c.1076G>A
NM_001406514.1:c.1076G>A
NM_001406515.1:c.1076G>A
NM_001406516.1:c.1076G>A
NM_001406517.1:c.980G>A
NM_001406518.1:c.980G>A
NM_001406519.1:c.1076G>A
NM_001406520.1:c.1076G>A
NM_001406521.1:c.1076G>A
NM_001406522.1:c.1076G>A
NM_001406523.1:c.1076G>A
NM_001406524.1:c.1076G>A
NM_001406525.1:c.1076G>A
NM_001406526.1:c.1076G>A
NM_001406527.1:c.1076G>A
NM_001406528.1:c.1076G>A
NM_001406530.1:c.980G>A
NM_001406531.1:c.1076G>A
NM_001406532.1:c.1076G>A
NM_001406534.1:c.1076G>A
NM_001406535.1:c.1076G>A
NM_001406536.1:c.980G>A
NM_001406537.1:c.1076G>A
NM_001406538.1:c.1076G>A
NM_001406539.1:c.707-60G>A
NM_001406540.1:c.1076G>A
NM_001406541.1:c.1076G>A
NM_001406542.1:c.1076G>A
NM_001406543.1:c.980G>A
NM_001406544.1:c.980G>A
NM_001406545.1:c.1076G>A
NM_001406546.1:c.1076G>A
NM_001406547.1:c.1076G>A
NM_001406548.1:c.1076G>A
NP_000044.2:p.Ser359Asn
NP_001005918.1:p.Ser359Asn
NP_001317507.1:p.Ser359Asn
NP_001317508.1:p.Ser359Asn
NP_001393440.1:p.Ser359Asn
NP_001393441.1:p.Ser359Asn
NP_001393442.1:p.Ser359Asn
NP_001393443.1:p.Ser359Asn
NP_001393444.1:p.Ser359Asn
NP_001393445.1:p.Ser359Asn
NP_001393446.1:p.Ser327Asn
NP_001393447.1:p.Ser327Asn
NP_001393448.1:p.Ser359Asn
NP_001393449.1:p.Ser359Asn
NP_001393450.1:p.Ser359Asn
NP_001393451.1:p.Ser359Asn
NP_001393452.1:p.Ser359Asn
NP_001393453.1:p.Ser359Asn
NP_001393454.1:p.Ser359Asn
NP_001393455.1:p.Ser359Asn
NP_001393456.1:p.Ser359Asn
NP_001393457.1:p.Ser359Asn
NP_001393459.1:p.Ser327Asn
NP_001393460.1:p.Ser359Asn
NP_001393461.1:p.Ser359Asn
NP_001393463.1:p.Ser359Asn
NP_001393464.1:p.Ser359Asn
NP_001393465.1:p.Ser327Asn
NP_001393466.1:p.Ser359Asn
NP_001393467.1:p.Ser359Asn
NP_001393469.1:p.Ser359Asn
NP_001393470.1:p.Ser359Asn
NP_001393471.1:p.Ser359Asn
NP_001393472.1:p.Ser327Asn
NP_001393473.1:p.Ser327Asn
NP_001393474.1:p.Ser359Asn
NP_001393475.1:p.Ser359Asn
NP_001393476.1:p.Ser359Asn
NP_001393477.1:p.Ser359Asn
NC_000013.10:g.52548280C>T
NM_000053.3:c.1076G>A

Protein change:

S327N

Molecular consequence:

NM_001243182.2:c.803-60G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406539.1:c.707-60G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000053.4:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406511.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406512.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406513.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406514.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406515.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406516.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406517.1:c.980G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406518.1:c.980G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406519.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406520.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406521.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406522.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406523.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406524.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406525.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406526.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406527.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406528.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406530.1:c.980G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406531.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406532.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406534.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406535.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406536.1:c.980G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406537.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406538.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406540.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406541.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406542.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406543.1:c.980G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406544.1:c.980G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406545.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406546.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406547.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406548.1:c.1076G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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Mus musculus RIKEN cDNA 2900026A02 gene (2900026A02Rik), mRNA
Mus musculus RIKEN cDNA 2900026A02 gene (2900026A02Rik), mRNA
gi|27370347|ref|NM_172884.1|

Nucleotide
103226[uid] AND (alive[prop]) (0)
Gene
CBWN15028.b1 NICHD_XGC_tropTe1 Xenopus tropicalis cDNA clone IMAGE:8920167 5', m...
CBWN15028.b1 NICHD_XGC_tropTe1 Xenopus tropicalis cDNA clone IMAGE:8920167 5', mRNA sequence
gi|133799450|gnl|dbEST|45229054|gb| 094.1|

Nucleotide
CBWN4026.b1 NICHD_XGC_tropTe1 Xenopus tropicalis cDNA clone IMAGE:8855977 5', mR...
CBWN4026.b1 NICHD_XGC_tropTe1 Xenopus tropicalis cDNA clone IMAGE:8855977 5', mRNA sequence
gi|133784120|gnl|dbEST|45213726|gb| 766.1|

Nucleotide
AGENCOURT_19145460 NICHD_XGC_Te2 Xenopus laevis cDNA clone IMAGE:7210926 5', mRN...
AGENCOURT_19145460 NICHD_XGC_Te2 Xenopus laevis cDNA clone IMAGE:7210926 5', mRNA sequence
gi|43392011|gnl|dbEST|21713947|gb|C 54.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004002677	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 21, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004002677

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 21, 2023)

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 Ambry Genetics, SCV004002677.2

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

Description

The p.S359N variant (also known as c.1076G>A), located in coding exon 2 of the ATP7B gene, results from a G to A substitution at nucleotide position 1076. The serine at codon 359 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration 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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