PRICKLE1

protein-coding

prickle planar cell polarity protein 1, the group of Prickle planar cell polarity proteins|LIM domain containing

Gene summary

This gene encodes a nuclear receptor that may be a negative regulator of the Wnt/beta-catenin signaling pathway. The encoded protein localizes to the nuclear membrane and has been implicated in the nuclear trafficking of the transcription repressors REST/NRSF and REST4. Mutations in this gene have been linked to progressive myoclonus epilepsy. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Sep 2009]

MANE transcript

NM_153026.3

Inheritance

AR, AD

ClinVar variants

P:2U:362B:178

Top phenotype

Epilepsy, progressive myoclonic, 1B

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr12:42,456,757-42,590,355

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~133.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

epilepsy, progressive myoclonic, 1BLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0012904

Submitter: PanelApp Australia

epilepsyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005027

Submitter: PanelApp Australia

Unverricht-Lundborg syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009698

Submitter: Orphanet

progressive myoclonus epilepsyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0020074

Submitter: ClinGen

*PRICKLE1* was first reported in relation to autosomal recessive progressive myoclonic epilepsy (PME) in 2008 when Bassuk et al. studied 3 large consanguineous Middle Eastern pedigrees with autosomal recessive PME without variants in *CSTB*, another gene associated with Unverricht-Lundborg syndrome (PMID: 18976727). These families were all found to have an identical homozygous p.Arg104Gln variant. Later in 2018, Mastrangelo M et al. identified another proband with a similar phenotypic presentation and the homozygous p.Ala274Thr variant (PMID: 30345727). Additional probands were identified in the literature; however, they were not scored based on atypical phenotypes not consistent with PME and the high minor allele frequency of the variants detected (PMID: 30564977, 37593999). Per criteria outlined by the ClinGen Lumping and Splitting guidelines, we found a difference in inheritance pattern and phenotypic variability. Therefore, the following disease entities have been split into two disease entities: autosomal recessive progressive myoclonic epilepsy (PME) and autosomal dominant epilepsy. The split curation for autosomal dominant epilepsy has been curated separately. Experimental evidence identified in the literature was not scored as it did not provide sufficient evidence supporting the gene-disease relationship. In summary, there is limited evidence to support the relationship between *PRICKLE1* and autosomal recessive progressive myoclonus epilepsy (PME). This classification was approved by the ClinGen Epilepsy GCEP on the meeting date July 1, 2025 (SOP Version 11).

epilepsyNO_KNOWN

Inheritance Pattern: AD

Disease ID:MONDO:0005027

Submitter: ClinGen

**Note: In September 2021, the ClinGen Epilepsy GCEP opted to change the disease term on this curation from Progressive Myoclonic Epilepsy to Epilepsy. The evidence summary below reflects this change. The original evidence and conclusion remains the same; therefore, the original date of approval has not been changed. ** PRICKLE1 was reported in relation to autosomal dominant progressive myoclonic epilepsy (PME) in 2019 by Algahtani et al (PMID: 31035234). However, the phenotype described, presence of unaffected carriers, and allele frequency of the variant identified were not consistent with AD PME. Additional probands in whom a heterozygous PRICKLE1 variant was identified had epileptic phenotypes inconsistent with PME (21276947, 31875159, 29790814). No case-level evidence supports this gene-disease relationship. Of note, one case of a de novo variant in PRICKLE1 causing autosomal dominant complex neurodevelopmental disorder, including a seizure phenotype, has been reported (29790814). PRICKLE1 has also been assessed for autosomal recessive progressive myoclonic epilepsy by the ClinGen Epilepsy Expert Panel and found to have a Limited classification. In summary, there is convincing evidence disputing the relationship between PRICKLE1 and autosomal dominant epilepsy. More evidence is needed to either support or refute the role PRICKLE1 plays in this disease. This classification was approved by the ClinGen Epilepsy Expert Panel on 9/1/2020.

epilepsy, progressive myoclonic, 1BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012904

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Epilepsy, progressive myoclonic, 1BAD/AR

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Comments: As with other forms of epilepsy, optimal seizure control is advantageous, and genetic diagnosis may aid with medication selection

Refs: 15634728; 15642921; 16376507; 18976727; 21276947Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRICKLE1 variants in ClinVar

11 Conditions Cataloged
Epilepsy, progressive myoclonic, 1BTotal: 499
not specifiedTotal: 175
not providedTotal: 138
PRICKLE1-related disorderTotal: 20
Self-limited epilepsy with centrotemporal spikesTotal: 3
Intellectual disabilityTotal: 3
Fetal akinesia deformation sequence 1Total: 1
SeizureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153026.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
165
clinvar
2
clinvar
171
missense
1
clinvar
1
clinvar
345
clinvar
8
clinvar
3
clinvar
358
nonsense
3
clinvar
3
start loss
1
clinvar
1
frameshift
9
clinvar
9
splice donor/acceptor (+/-2bp)
0
Total113621735542

Highest pathogenic variant AF is 0.000016108426

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 84 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_153026.3RefSeqNP_694571.27MANE Select
ENST00000345127.9EnsemblENSP00000345064.37MANE Select
NM_001144881.2RefSeqNP_001138353.17Standard
NM_001144882.2RefSeqNP_001138354.17Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
prickle1aDanio rerio

Structure: hepatocyte

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Wnt signaling pathway - Homo sapiens (human)
  • Wnt Signaling Pathway
  • Signaling by WNT
  • Signal Transduction
  • Asymmetric localization of PCP proteins

Biological Process

  • neural tube closure
  • protein import into nucleus
  • positive regulation of protein ubiquitination
  • positive regulation of proteasomal ubiquitin-dependent protein catabolic process
  • aorta development

Molecular Function

  • protein binding
  • zinc ion binding

Cellular Component

  • nucleus
  • cytosol
  • nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000455697
Coding exons
7
Length
132018
Individuals with no LoFs
125737
Homozygous LoFs
0
Heterozygous LoFs
8
Defined
125745
p
0.0000318
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.833484580.7590.00002685482
Missense (PolyPhen)102176.960.576412053
Synonymous0.9051621770.9140.00001071552
Loss of Function5.47136.80.02710.00000197445

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000630.000062rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000350.000035rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Involved in the planar cell polarity pathway that controls convergent extension during gastrulation and neural tube closure. Convergent extension is a complex morphogenetic process during which cells elongate, move mediolaterally, and intercalate between neighboring cells, leading to convergence toward the mediolateral axis and extension along the anteroposterior axis. Necessary for nuclear localization of REST. May serve as nuclear receptor. {ECO:0000269|PubMed:21901791}.;
Disease
DISEASE: Neural tube defects (NTD) [MIM:182940]: Congenital malformations of the central nervous system and adjacent structures related to defective neural tube closure during the first trimester of pregnancy. Failure of neural tube closure can occur at any level of the embryonic axis. Common NTD forms include anencephaly, myelomeningocele and spina bifida, which result from the failure of fusion in the cranial and spinal region of the neural tube. NTDs have a multifactorial etiology encompassing both genetic and environmental components. {ECO:0000269|PubMed:21901791}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.146

Intolerance Scores

LoFtool
0.0772
RVIS EVS
-0.29
RVIS percentile EVS
33.47

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.632

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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