NM_153026.3(PRICKLE1):c.356G>C (p.Arg119Thr) AND Epilepsy, progressive myoclonic, 1B

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 26, 2019
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:: RCV001039630.6

Allele description

NM_153026.3(PRICKLE1):c.356G>C (p.Arg119Thr)

Gene:

PRICKLE1:prickle planar cell polarity protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q12

Genomic location:

Preferred name:

NM_153026.3(PRICKLE1):c.356G>C (p.Arg119Thr)

HGVS:

NC_000012.12:g.42469478C>G
NG_012965.1:g.125293G>C
NM_001144881.2:c.356G>C
NM_001144882.2:c.356G>C
NM_001144883.2:c.356G>C
NM_153026.3:c.356G>CMANE SELECT
NP_001138353.1:p.Arg119Thr
NP_001138354.1:p.Arg119Thr
NP_001138355.1:p.Arg119Thr
NP_694571.2:p.Arg119Thr
NC_000012.11:g.42863280C>G
NM_153026.2:c.356G>C

Protein change:

R119T

Links:

dbSNP: rs961991320

NCBI 1000 Genomes Browser:

rs961991320

Molecular consequence:

NM_001144881.2:c.356G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144882.2:c.356G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144883.2:c.356G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_153026.3:c.356G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Epilepsy, progressive myoclonic, 1B
Synonyms:: Progressive myoclonus epilepsy with ataxia; PME
Identifiers:: MONDO: MONDO:0012904; MedGen: C2676254; Orphanet: 308; OMIM: 612437

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001203167	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 26, 2019)	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

SCV001203167

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 26, 2019)

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, SCV001203167.5

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C65"). 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. This variant has not been reported in the literature in individuals with PRICKLE1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with threonine at codon 119 of the PRICKLE1 protein (p.Arg119Thr). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and threonine.

#	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: Feb 28, 2024

ClinVar

Relating variation to medicine