NM_000053.4(ATP7B):c.2621C>T (p.Ala874Val) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Feb 16, 2022
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:: RCV001091639.31

Allele description [Variation Report for NM_000053.4(ATP7B):c.2621C>T (p.Ala874Val)]

NM_000053.4(ATP7B):c.2621C>T (p.Ala874Val)

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.2621C>T (p.Ala874Val)

HGVS:

NC_000013.11:g.51950116G>A
NG_008806.1:g.66379C>T
NM_000053.4:c.2621C>TMANE SELECT
NM_001005918.3:c.2135C>T
NM_001243182.2:c.2288C>T
NM_001330578.2:c.2387C>T
NM_001330579.2:c.2369C>T
NP_000044.2:p.Ala874Val
NP_001005918.1:p.Ala712Val
NP_001230111.1:p.Ala763Val
NP_001317507.1:p.Ala796Val
NP_001317508.1:p.Ala790Val
NC_000013.10:g.52524252G>A
NM_000053.3:c.2621C>T
P35670:p.Ala874Val

Protein change:

A712V; ALA874VAL

Links:

UniProtKB: P35670#VAR_000737; OMIM: 606882.0016; dbSNP: rs121907994

NCBI 1000 Genomes Browser:

rs121907994

Molecular consequence:

NM_000053.4:c.2621C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001005918.3:c.2135C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001243182.2:c.2288C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330578.2:c.2387C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330579.2:c.2369C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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nonsense-mediated mRNA decay factor SMG8 [Homo sapiens]
nonsense-mediated mRNA decay factor SMG8 [Homo sapiens]
gi|47777319|ref|NP_060619.4|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001247798	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Aug 1, 2017)	germline	clinical testing	Citation Link,
SCV001716163	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 20, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22692182, 22240481, 25741868
SCV001781887	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 9, 2020)	germline	clinical testing	Citation Link,
SCV002501994	AiLife Diagnostics, AiLife Diagnostics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 16, 2022)	germline	clinical testing	PubMed (18) [See all records that cite these PMIDs] 9452121, 26269689, 32911910, 29961769, 30655162, 25988284, 33763395, 31743419, 31980526, 22240481, 10721669, 30702195, 22692182, 24253677, 29381936, 28212618, 30275481, 25741868

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	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

Mutations of ATP7B gene in Wilson disease in Japan: identification of nine mutations and lack of clear founder effect in a Japanese population.

Yamaguchi A, Matsuura A, Arashima S, Kikuchi Y, Kikuchi K.

Hum Mutat. 1998;Suppl 1:S320-2. No abstract available.

PubMed [citation]

PMID:: 9452121

Wilson disease with hepatic presentation in an eight-month-old boy.

Abuduxikuer K, Li LT, Qiu YL, Wang NL, Wang JS.

World J Gastroenterol. 2015 Aug 7;21(29):8981-4. doi: 10.3748/wjg.v21.i29.8981.

PubMed [citation]

PMID:: 26269689
PMCID:: PMC4528042

See all PubMed Citations (18)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001247798.26

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV001716163.2

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

#	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

From GeneDx, SCV001781887.1

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

Description

Published functional studies using the baculovirus expression system in Sf9 cells showed partial transport activity (Huster et al. 2012); 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: 30275481, 31980526, 31743419, 9452121, 30702195, 30655162, 29961769, 11775208, 21707886, 10544227, 12544487, 27398169, 16998622, 22735241, 11043508, 28515472, 16207219, 25704634, 23275100, 22308153, 22484412, 26782526, 19419418, 29381936, 28212618, 26269689, 22692182, 10721669, 22240481, 24253677, 26215059, 25988284, 12376745, 18156766)

#	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 AiLife Diagnostics, AiLife Diagnostics, SCV002501994.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (18)

#	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		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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