NM_000052.7(ATP7A):c.2208T>C (p.Tyr736=) AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Nov 17, 2023
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:: RCV000553859.8

Allele description [Variation Report for NM_000052.7(ATP7A):c.2208T>C (p.Tyr736=)]

NM_000052.7(ATP7A):c.2208T>C (p.Tyr736=)

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.2208T>C (p.Tyr736=)

HGVS:

NC_000023.11:g.78012914T>C
NG_013224.2:g.107218T>C
NM_000052.7:c.2208T>CMANE SELECT
NM_001282224.2:c.2172+1240T>C
NP_000043.4:p.Tyr736=
NC_000023.10:g.77268411T>C
NM_000052.6:c.2208T>C

Links:

dbSNP: rs1557234725

NCBI 1000 Genomes Browser:

rs1557234725

Molecular consequence:

NM_001282224.2:c.2172+1240T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000052.7:c.2208T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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

Recent activity

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Sinorhizobium meliloti AK11 contig_275, whole genome shotgun sequence
Sinorhizobium meliloti AK11 contig_275, whole genome shotgun sequence
gi|400340328|gb|AKZV01000275.1||gnl AKZV01|contig_275

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000639971	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Nov 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000639971

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Nov 17, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV000639971.5

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

#	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

Last Updated: Sep 29, 2024

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