NM_145239.3(PRRT2):c.802_804del (p.Tyr268del) AND Episodic kinesigenic dyskinesia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 16, 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:: RCV002534978.10

Allele description [Variation Report for NM_145239.3(PRRT2):c.802_804del (p.Tyr268del)]

NM_145239.3(PRRT2):c.802_804del (p.Tyr268del)

Genes:

MVP-DT:MVP divergent transcript [Gene - HGNC]
PRRT2:proline rich transmembrane protein 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

NM_145239.3(PRRT2):c.802_804del (p.Tyr268del)

HGVS:

NC_000016.10:g.29813856_29813858del
NG_032039.1:g.6769_6771del
NM_001256442.2:c.802_804del
NM_001256443.2:c.802_804del
NM_145239.3:c.802_804delMANE SELECT
NP_001243371.1:p.Tyr268del
NP_001243372.1:p.Tyr268del
NP_660282.2:p.Tyr268del
NC_000016.9:g.29825175_29825177del
NC_000016.9:g.29825177_29825179del
NM_145239.2:c.802_804delTAC

Protein change:

Y268del

Links:

dbSNP: rs1567380086

NCBI 1000 Genomes Browser:

rs1567380086

Molecular consequence:

NM_001256442.2:c.802_804del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001256443.2:c.802_804del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_145239.3:c.802_804del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

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

Recent activity

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Homo sapiens nitric oxide synthase 2 (NOS2), mRNA
Homo sapiens nitric oxide synthase 2 (NOS2), mRNA
gi|206597519|ref|NM_000625.4|

Nucleotide
Homo sapiens stonin 1 (STON1), transcript variant 2, mRNA
Homo sapiens stonin 1 (STON1), transcript variant 2, mRNA
gi|1813772506|ref|NM_006873.4|

Nucleotide
Pseudoalteromonas sp. JSTW chromosome, complete genome
Pseudoalteromonas sp. JSTW chromosome, complete genome
gi|1874562094|gb|CP058972.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003199801	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 16, 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

SCV003199801

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 16, 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, SCV003199801.2

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

Description

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 589991). This variant, c.802_804del, results in the deletion of 1 amino acid(s) of the PRRT2 protein (p.Tyr268del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PRRT2-related conditions.

#	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: Oct 26, 2024

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