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

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 26, 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:: RCV001388947.1

Allele description

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

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:

Deletion

Cytogenetic location:

16p11.2

Genomic location:

Chr16: 29802081 - 30200285 (on Assembly GRCh37)

Preferred name:

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

HGVS:

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

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
SCV001590123	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 26, 2020)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 22515636, 23363396, 24811917, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001590123

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 26, 2020)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Microdeletions detected using chromosome microarray in children with suspected genetic movement disorders: a single-centre study.

Dale RC, Grattan-Smith P, Nicholson M, Peters GB.

Dev Med Child Neurol. 2012 Jul;54(7):618-23. doi: 10.1111/j.1469-8749.2012.04287.x. Epub 2012 Apr 19.

PubMed [citation]

PMID:: 22515636

Clinical features of childhood-onset paroxysmal kinesigenic dyskinesia with PRRT2 gene mutations.

Silveira-Moriyama L, Gardiner AR, Meyer E, King MD, Smith M, Rakshi K, Parker A, Mallick AA, Brown R, Vassallo G, Jardine PE, Guerreiro MM, Lees AJ, Houlden H, Kurian MA.

Dev Med Child Neurol. 2013 Apr;55(4):327-34. doi: 10.1111/dmcn.12056. Epub 2013 Jan 30.

PubMed [citation]

PMID:: 23363396

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001590123.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the PRRT2 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Loss-of-function variants in PRRT2 are known to be pathogenic. This particular deletion has been reported in the literature in individuals affected with paroxysmal kinesigenic dyskinesia, infantile convulsions with paroxysmal choreoathetosis syndrome, and/or epilepsy (PMID: 22515636, 23363396, 24811917). For these reasons, this variant has been classified as Pathogenic.

#	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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