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NM_000052.7(ATP7A):c.4356G>C (p.Leu1452Phe) AND multiple conditions

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Oct 4, 2023
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:
RCV000792466.6

Allele description [Variation Report for NM_000052.7(ATP7A):c.4356G>C (p.Leu1452Phe)]

NM_000052.7(ATP7A):c.4356G>C (p.Leu1452Phe)

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.4356G>C (p.Leu1452Phe)
HGVS:
  • NC_000023.11:g.78046423G>C
  • NG_013224.2:g.140727G>C
  • NM_000052.7:c.4356G>CMANE SELECT
  • NM_001282224.2:c.4122G>C
  • NP_000043.4:p.Leu1452Phe
  • NP_001269153.1:p.Leu1374Phe
  • NC_000023.10:g.77301920G>C
  • NM_000052.6:c.4356G>C
  • NR_104109.2:n.1529G>C
Protein change:
L1374F
Links:
dbSNP: rs782364202
NCBI 1000 Genomes Browser:
rs782364202
Molecular consequence:
  • NM_000052.7:c.4356G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282224.2:c.4122G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104109.2:n.1529G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000931767Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Oct 4, 2023)
germlineclinical testing

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

SCV002783988Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Aug 13, 2021)
unknownclinical testing

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

Summary from all submissions

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

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 Invitae, SCV000931767.4

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

From Fulgent Genetics, Fulgent Genetics, SCV002783988.1

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

Last Updated: Jul 23, 2024