NM_145239.3(PRRT2):c.647C>G (p.Pro216Arg) AND Inborn genetic diseases

Germline classification:: Likely benign (1 submission)
Last evaluated:: Feb 29, 2024
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:: RCV002354247.9

Allele description [Variation Report for NM_145239.3(PRRT2):c.647C>G (p.Pro216Arg)]

NM_145239.3(PRRT2):c.647C>G (p.Pro216Arg)

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.647C>G (p.Pro216Arg)

Other names:

p.P216R:CCC>CGC

HGVS:

NC_000016.10:g.29813701C>G
NG_032039.1:g.6614C>G
NM_001256442.2:c.647C>G
NM_001256443.2:c.647C>G
NM_145239.3:c.647C>GMANE SELECT
NP_001243371.1:p.Pro216Arg
NP_001243372.1:p.Pro216Arg
NP_660282.2:p.Pro216Arg
NC_000016.9:g.29825022C>G
NM_145239.2:c.647C>G

Protein change:

P216R

Links:

dbSNP: rs76335820

NCBI 1000 Genomes Browser:

rs76335820

Molecular consequence:

NM_001256442.2:c.647C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001256443.2:c.647C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_145239.3:c.647C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002656047	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Feb 29, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23190448, 25502464, 26598493 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002656047

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Feb 29, 2024)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

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

Novel PRRT2 mutations in paroxysmal dyskinesia patients with variant inheritance and phenotypes.

Liu XR, Wu M, He N, Meng H, Wen L, Wang JL, Zhang MP, Li WB, Mao X, Qin JM, Li BM, Tang B, Deng YH, Shi YW, Su T, Yi YH, Tang BS, Liao WP.

Genes Brain Behav. 2013 Mar;12(2):234-40. doi: 10.1111/gbb.12008. Epub 2012 Dec 21.

PubMed [citation]

PMID:: 23190448

Identification of a Premature Termination Mutation in the Proline-Rich Transmembrane Protein 2 Gene in a Chinese Family with Febrile Seizures.

Zheng W, Zhang J, Deng X, Xiao J, Yuan L, Yang Y, Guan L, Song Z, Yang Z, Deng H.

Mol Neurobiol. 2016 Mar;53(2):835-841. doi: 10.1007/s12035-014-9047-4. Epub 2014 Dec 15.

PubMed [citation]

PMID:: 25502464

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV002656047.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: May 1, 2024

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