NM_000052.7(ATP7A):c.1947-3_1948dup AND Menkes disease, copper-replacement responsive

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 1, 2003
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000012556.17

Allele description [Variation Report for NM_000052.7(ATP7A):c.1947-3_1948dup]

NM_000052.7(ATP7A):c.1947-3_1948dup

Gene:

ATP7A:ATPase copper transporting alpha [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xq21.1

Genomic location:

Preferred name:

NM_000052.7(ATP7A):c.1947-3_1948dup

HGVS:

NC_000023.11:g.78011446_78011450dup
NG_013224.2:g.105750_105754dup
NM_000052.6:c.1947-3_1948dupAAGAT
NM_000052.7:c.1947-3_1948dupMANE SELECT
NM_001282224.2:c.1947-3_1948dup
NC_000023.10:g.77266943_77266947dup

Note:

NCBI staff provided HGVS expressions for allelic variant 300011.0010 from these descriptions: (1) "...IVS8,AS,dup5, indicating the location of the duplication at the acceptor site (AS) of intron 8 (IVS8) from Kaler et al., 1996 (PubMed 8812725) and (2) "Sequencing of the patient's genomic DNA revealed a direct duplication of five bases (ATAAG) at the splice acceptor site preceding a 226-bp exon." from Das et al., 1994 (PubMed 7977350). The 226 bp exon corresponds to NG_013224.2:exon 9.

Nucleotide change:

EX8 DEL

Links:

OMIM: 300011.0010

Molecular consequence:

NM_000052.7:c.1947-3_1948dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001282224.2:c.1947-3_1948dup - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Menkes disease, copper-replacement responsive
Identifiers:: MedGen: C4016447

Recent activity

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PREDICTED: Populus trichocarpa squamosa promoter-binding-like protein 1 (LOC7481...
PREDICTED: Populus trichocarpa squamosa promoter-binding-like protein 1 (LOC7481436), transcript variant X2, mRNA
gi|2396437521|ref|XM_024594312.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000032790	OMIM	no assertion criteria provided	Pathogenic (Apr 1, 2003)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 8812725, 12676902

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000032790

OMIM

no assertion criteria provided

Pathogenic
(Apr 1, 2003)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Successful early copper therapy in Menkes disease associated with a mutant transcript containing a small In-frame deletion.

Kaler SG, Das S, Levinson B, Goldstein DS, Holmes CS, Patronas NJ, Packman S, Gahl WA.

Biochem Mol Med. 1996 Feb;57(1):37-46.

PubMed [citation]

PMID:: 8812725

A copper treatable Menkes disease mutation associated with defective trafficking of a functional Menkes copper ATPase.

Kim BE, Smith K, Petris MJ.

J Med Genet. 2003 Apr;40(4):290-5. No abstract available.

PubMed [citation]

PMID:: 12676902
PMCID:: PMC1735426

Details of each submission

From OMIM, SCV000032790.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

Kaler et al. (1996) described successful early copper therapy in Menkes disease (309400) associated with a mutant transcript containing a small in-frame deletion. This splice site mutation resulted in deletion of exon 8, which encodes a small region between the sixth copper binding site and the first membrane-spanning domain of MNK protein. Kim et al. (2003) demonstrated that the mutant protein was defective in copper-induced trafficking but its copper transport mutant function was retained. The sequence of exon 8 was deleted from the mutant protein extended between serine-624 and glutamine-649 that was deleted in the in-frame transcript of the patient and replaced by 624 ile-arg.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 16, 2023

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