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NM_000052.7(ATP7A):c.2406+16_2406+18del AND multiple conditions

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 21, 2024
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:
RCV002134651.6

Allele description [Variation Report for NM_000052.7(ATP7A):c.2406+16_2406+18del]

NM_000052.7(ATP7A):c.2406+16_2406+18del

Gene:
ATP7A:ATPase copper transporting alpha [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq21.1
Genomic location:
Preferred name:
NM_000052.7(ATP7A):c.2406+16_2406+18del
HGVS:
  • NC_000023.11:g.78013128_78013130del
  • NG_013224.2:g.107432_107434del
  • NM_000052.7:c.2406+16_2406+18delMANE SELECT
  • NM_001282224.2:c.2172+1454_2172+1456del
  • NC_000023.10:g.77268624_77268626del
  • NC_000023.10:g.77268625_77268627del
Links:
dbSNP: rs782017566
NCBI 1000 Genomes Browser:
rs782017566
Molecular consequence:
  • NM_000052.7:c.2406+16_2406+18del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282224.2:c.2172+1454_2172+1456del - intron variant - [Sequence Ontology: SO:0001627]

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
Name:
Cutis laxa, X-linked (OHS)
Synonyms:
EDS IX; Occipital horn syndrome; Ehlers-Danlos syndrome, occipital horn type (formerly); See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010572; MedGen: C0268353; Orphanet: 198; OMIM: 304150
Name:
X-linked distal spinal muscular atrophy type 3
Synonyms:
SPINAL MUSCULAR ATROPHY, DISTAL, X-LINKED RECESSIVE; NEURONOPATHY, DISTAL HEREDITARY MOTOR, X-LINKED; NEUROPATHY, DISTAL HEREDITARY MOTOR, X-LINKED
Identifiers:
MONDO: MONDO:0010338; MedGen: C1845359; Orphanet: 139557; OMIM: 300489

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002412089Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Jan 21, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002412089.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024