NC_000016.9:g.(?_29802081)_(30200285_?)dup AND Episodic kinesigenic dyskinesia

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 24, 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:: RCV001325791.1

Allele description

NC_000016.9:g.(?_29802081)_(30200285_?)dup

Genes:

CDIPT:CDP-diacylglycerol--inositol 3-phosphatidyltransferase [Gene - OMIM - HGNC]
HIRIP3:HIRA interacting protein 3 [Gene - OMIM - HGNC]
INO80E:INO80 complex subunit E [Gene - HGNC]
MAZ:MYC associated zinc finger protein [Gene - OMIM - HGNC]
PAGR1:PAXIP1 associated glutamate rich protein 1 [Gene - OMIM - HGNC]
TBX6:T-box transcription factor 6 [Gene - OMIM - HGNC]
TAOK2:TAO kinase 2 [Gene - OMIM - HGNC]
TLCD3B:TLC domain containing 3B [Gene - OMIM - HGNC]
ALDOA:aldolase, fructose-bisphosphate A [Gene - OMIM - HGNC]
ASPHD1:aspartate beta-hydroxylase domain containing 1 [Gene - HGNC]
C16orf92:chromosome 16 open reading frame 92 [Gene - OMIM - HGNC]
CORO1A:coronin 1A [Gene - OMIM - HGNC]
DOC2A:double C2 domain alpha [Gene - OMIM - HGNC]
GDPD3:glycerophosphodiester phosphodiesterase domain containing 3 [Gene - OMIM - HGNC]
KIF22:kinesin family member 22 [Gene - OMIM - HGNC]
MVP:major vault protein [Gene - OMIM - HGNC]
MAPK3:mitogen-activated protein kinase 3 [Gene - OMIM - HGNC]
KCTD13:potassium channel tetramerization domain containing 13 [Gene - OMIM - HGNC]
PRRT2:proline rich transmembrane protein 2 [Gene - OMIM - HGNC]
PPP4C:protein phosphatase 4 catalytic subunit [Gene - OMIM - HGNC]
SEZ6L2:seizure related 6 homolog like 2 [Gene - OMIM - HGNC]
TMEM219:transmembrane protein 219 [Gene - HGNC]
YPEL3:yippee like 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16p11.2

Genomic location:

Chr16: 29802081 - 30200285 (on Assembly GRCh37)

Preferred name:

NC_000016.9:g.(?_29802081)_(30200285_?)dup

HGVS:

NC_000016.9:g.(?_29802081)_(30200285_?)dup

Condition(s)

Name:: Episodic kinesigenic dyskinesia (EKD)
Synonyms:: Familial paroxysmal dystonia; Paroxysmal kinesigenic dyskinesia
Identifiers:: MONDO: MONDO:0044202; MedGen: C1868682; Orphanet: 98809; OMIM: PS128200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001516796	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 24, 2020)	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

SCV001516796

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 24, 2020)

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 Invitae, SCV001516796.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the PRRT2 gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has been observed to be homozygous or hemizygous in an individual who was not affected with PRRT2-related disease (Invitae). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Apr 23, 2022

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