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NM_000052.7(ATP7A):c.2048A>G (p.His683Arg) AND Menkes kinky-hair syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 11, 2020
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:
RCV002471710.1

Allele description [Variation Report for NM_000052.7(ATP7A):c.2048A>G (p.His683Arg)]

NM_000052.7(ATP7A):c.2048A>G (p.His683Arg)

Gene:
ATP7A:ATPase copper transporting alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq21.1
Genomic location:
Preferred name:
NM_000052.7(ATP7A):c.2048A>G (p.His683Arg)
HGVS:
  • NC_000023.11:g.78011550A>G
  • NG_013224.2:g.105854A>G
  • NM_000052.7:c.2048A>GMANE SELECT
  • NM_001282224.2:c.2048A>G
  • NP_000043.4:p.His683Arg
  • NP_001269153.1:p.His683Arg
  • NC_000023.10:g.77267047A>G
  • NM_000052.6:c.2048A>G
Protein change:
H683R
Molecular consequence:
  • NM_000052.7:c.2048A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282224.2:c.2048A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Menkes kinky-hair syndrome (MNK)
Synonyms:
Kinky hair disease; Copper transport disease; Menkes Disease
Identifiers:
MONDO: MONDO:0010651; MedGen: C0022716; Orphanet: 565; OMIM: 309400

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002769191Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jun 11, 2020) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002769191.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3C-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0109 - This gene is known to be associated with X-linked recessive disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from a histidine to an arginine (exon 9). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (2 heterozygotes, 0 homozygotes). (N) 0503 - Missense variant consistently predicted to be tolerated or not conserved in mammals with a minor amino acid change. (B) 0600 - Variant is located in an annotated domain or motif (P-type_ATPase_Cu-like domain; NCBI). (N) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1205 - Variant is maternally inherited. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024