PRICKLE1
protein-codingprickle 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~133.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012904
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0005027
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009698
Submitter: Orphanet
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).
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.
Inheritance Pattern: AR
Disease ID:MONDO:0012904
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRICKLE1 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 165 | 2 | 171 | ||
| missense | 1 | 1 | 345 | 8 | 3 | 358 |
| nonsense | 3 | 3 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 9 | 9 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 1 | 362 | 173 | 5 | 542 |
Highest pathogenic variant AF is 0.000016108426
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_694571.2 | 7 | MANE Select | |
| Ensembl | ENSP00000345064.3 | 7 | MANE Select | |
| RefSeq | NP_001138353.1 | 7 | Standard | |
| RefSeq | NP_001138354.1 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| prickle1a | Danio 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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.83 | 348 | 458 | 0.759 | 0.0000268 | 5482 |
| Missense (PolyPhen) | 102 | 176.96 | 0.57641 | 2053 | ||
| Synonymous | 0.905 | 162 | 177 | 0.914 | 0.0000107 | 1552 |
| Loss of Function | 5.47 | 1 | 36.8 | 0.0271 | 0.00000197 | 445 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000063 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |