NM_145239.3(PRRT2):c.718C>T (p.Arg240Ter) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000431690.9

Allele description [Variation Report for NM_145239.3(PRRT2):c.718C>T (p.Arg240Ter)]

NM_145239.3(PRRT2):c.718C>T (p.Arg240Ter)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

NM_145239.3(PRRT2):c.718C>T (p.Arg240Ter)

HGVS:

NC_000016.10:g.29813772C>T
NG_032039.1:g.6685C>T
NM_001256442.2:c.718C>T
NM_001256443.2:c.718C>T
NM_145239.3:c.718C>TMANE SELECT
NP_001243371.1:p.Arg240Ter
NP_001243372.1:p.Arg240Ter
NP_660282.2:p.Arg240Ter
NC_000016.9:g.29825093C>T
NM_145239.2:c.718C>T

Protein change:

R240*; ARG240TER

Links:

OMIM: 614386.0007; dbSNP: rs387907126

NCBI 1000 Genomes Browser:

rs387907126

Molecular consequence:

NM_001256442.2:c.718C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001256443.2:c.718C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_145239.3:c.718C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000516081	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Mar 24, 2015)	germline	clinical testing	Citation Link,
SCV004701572	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jan 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000516081

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Mar 24, 2015)

germline

clinical testing

Citation Link,

SCV004701572

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jan 1, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000516081.4

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

Description

The R240X nonsense variant in the PRRT2 gene has been reported previously in association with paroxysmal kinesigenic dyskinesia with infantile convulsions (PKD/IC), PKD with migraines without aura, and benign familial infantile seizures (BFIS) (Lee et al., 2012; Cloarec et al., 2012; Labate et al., 2013). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. We interpret this variant as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004701572.8

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

Description

PRRT2: PVS1, PP1:Strong, PM2, PS4:Moderate

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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