NM_000053.4(ATP7B):c.4135C>T (p.Pro1379Ser) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Sep 9, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000587055.43

Allele description [Variation Report for NM_000053.4(ATP7B):c.4135C>T (p.Pro1379Ser)]

NM_000053.4(ATP7B):c.4135C>T (p.Pro1379Ser)

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.4135C>T (p.Pro1379Ser)

HGVS:

NC_000013.11:g.51935019G>A
NG_008806.1:g.81476C>T
NM_000053.4:c.4135C>TMANE SELECT
NM_001005918.3:c.3514C>T
NM_001243182.2:c.3802C>T
NM_001330578.2:c.3901C>T
NM_001330579.2:c.3883C>T
NP_000044.2:p.Pro1379Ser
NP_001005918.1:p.Pro1172Ser
NP_001230111.1:p.Pro1268Ser
NP_001317507.1:p.Pro1301Ser
NP_001317508.1:p.Pro1295Ser
NC_000013.10:g.52509155G>A
NM_000053.2:c.4135C>T
NM_000053.3:c.4135C>T
NM_001005918.2:c.3514C>T
P35670:p.Pro1379Ser

Protein change:

P1172S

Links:

UniProtKB: P35670#VAR_044494; dbSNP: rs181250704

NCBI 1000 Genomes Browser:

rs181250704

Molecular consequence:

NM_000053.4:c.4135C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.3514C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.3802C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.3901C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.3883C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

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
SCV000331180	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (May 17, 2017)	germline	clinical testing	Citation Link,
SCV000520721	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 9, 2024)	germline	clinical testing	Citation Link,
SCV001156175	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV001713626	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 8, 2019)	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	3	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	7	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 Eurofins Ntd Llc (ga), SCV000331180.4

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

#	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		5	not provided	not provided	not provided

From GeneDx, SCV000520721.9

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

Description

Functional analysis found that it is associated with normal transport activity and trafficking (PMID: 21454443); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 14962673, 28392828, 25741868, 16472602, 33848968, 32685348, 17680703, 32248359, 34426522, 24253677, 30254379, 30097039, 23430806, 35626323, 34620762, 16088907, 21454443, 37660282, 33972609, 37937776, 30476936)

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001156175.27

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

Description

ATP7B: BS2

#	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		3	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001713626.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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	germline	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine