PRICKLE2-AS1

Summary

PRICKLE2-AS1 (PRICKLE2 antisense RNA 1, HGNC:40916) is a long non-coding RNA gene on chromosome 3p14.1.

At a glance

• Clinical variants (ClinVar): 77 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40916
Approved symbol	PRICKLE2-AS1
Name	PRICKLE2 antisense RNA 1
Location	3p14.1
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000241572
Entrez	100652759
RNAcentral	URS000075DA3C — lncRNA, 6521 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Bgee: expression breadth broad, 86 present calls, max score 84.18.

Top tissues by expression

86 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.18	gold quality
hindlimb stylopod muscle	UBERON:0004252	68.31	gold quality
ganglionic eminence	UBERON:0004023	63.97	gold quality
right testis	UBERON:0004534	61.62	gold quality
left testis	UBERON:0004533	61.37	gold quality
testis	UBERON:0000473	60.89	gold quality
ventricular zone	UBERON:0003053	60.09	gold quality
cortex of kidney	UBERON:0001225	56.62	gold quality
smooth muscle tissue	UBERON:0001135	56.29	gold quality
kidney	UBERON:0002113	56.10	gold quality
prefrontal cortex	UBERON:0000451	55.96	gold quality
stromal cell of endometrium	CL:0002255	55.47	gold quality
islet of Langerhans	UBERON:0000006	55.36	gold quality
endocervix	UBERON:0000458	54.02	gold quality
endometrium	UBERON:0001295	53.53	gold quality
heart left ventricle	UBERON:0002084	52.95	gold quality
liver	UBERON:0002107	52.73	silver quality
muscle of leg	UBERON:0001383	52.62	gold quality
monocyte	CL:0000576	52.21	gold quality
gastrocnemius	UBERON:0001388	52.08	gold quality
blood	UBERON:0000178	51.66	silver quality
heart	UBERON:0000948	50.13	gold quality
pancreas	UBERON:0001264	49.36	gold quality
adult mammalian kidney	UBERON:0000082	49.04	gold quality
right lobe of liver	UBERON:0001114	48.90	silver quality
multicellular organism	UBERON:0000468	48.74	gold quality
right lung	UBERON:0002167	48.01	gold quality
tibial artery	UBERON:0007610	47.70	gold quality
stomach	UBERON:0000945	47.31	gold quality
left coronary artery	UBERON:0001626	47.25	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (0):

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chr3p14, CBX5_TARGET_GENES, DESCARTES_MAIN_FETAL_PHOTORECEPTOR_CELLS, DESCARTES_FETAL_ADRENAL_SLC26A4_PAEP_POSITIVE_CELLS, DESCARTES_FETAL_EYE_PHOTORECEPTOR_CELLS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

77 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	22
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

176 predictions. Top by Δscore:

Variant	Effect	Δscore
3:64099923:GGCCT:G	acceptor_loss	1.0000
3:64099925:CCT:C	acceptor_loss	1.0000
3:64099927:T:A	acceptor_loss	1.0000
3:64099086:T:TA	donor_gain	0.9900
3:64099921:GAGGC:G	acceptor_gain	0.9900
3:64099922:AGGC:A	acceptor_gain	0.9900
3:64099923:GGC:G	acceptor_gain	0.9900
3:64099924:GC:G	acceptor_gain	0.9900
3:64099925:CC:C	acceptor_gain	0.9900
3:64099926:C:CC	acceptor_gain	0.9900
3:64099063:A:AC	donor_gain	0.9800
3:64099064:C:CC	donor_gain	0.9800
3:64099077:T:TA	donor_gain	0.9700
3:64099109:C:CT	donor_gain	0.9700
3:64099926:C:T	acceptor_gain	0.9700
3:64099105:TCTGC:T	donor_gain	0.9400
3:64099106:CTGCC:C	donor_gain	0.9400
3:64099385:T:A	donor_gain	0.9400
3:64099107:TGC:T	donor_gain	0.9100
3:64102708:T:TA	donor_gain	0.8400
3:64099448:T:C	donor_gain	0.8200
3:64099007:CATT:C	donor_gain	0.7700
3:64099110:C:CT	donor_gain	0.7600
3:64099008:A:C	donor_gain	0.7500
3:64099002:CT:C	donor_gain	0.7300
3:64099003:TT:T	donor_gain	0.7300
3:64099004:TT:T	donor_gain	0.7300
3:64099064:CAGTT:C	donor_gain	0.7200
3:64099064:CA:C	donor_gain	0.7000
3:64099675:T:TA	donor_gain	0.6800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000059461 (3:64080805 G>A), RS1000090309 (3:64081100 T>C), RS1000218064 (3:64094345 T>C), RS1000364628 (3:64086498 C>A), RS1000378311 (3:64068641 T>G), RS1000462173 (3:64100663 T>C), RS1000554087 (3:64095701 C>A,G,T), RS1000634797 (3:64095381 T>C), RS1000640976 (3:64087760 T>C), RS1000727933 (3:64097460 T>A), RS1000785307 (3:64090855 C>T), RS1000900408 (3:64090976 C>T), RS1000973198 (3:64085055 C>G,T), RS1001065730 (3:64079449 A>G), RS1001095167 (3:64079663 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:254800

GenCC curated gene-disease

Mondo (2): myoclonic epilepsy (MONDO:0100577), progressive myoclonus epilepsy (MONDO:0020074)

Orphanet (3): Progressive myoclonic epilepsy type 5 (Orphanet:402082), Progressive myoclonic epilepsy type 1 (Orphanet:308), Progressive myoclonic epilepsy (Orphanet:98261)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D020191	Myoclonic Epilepsies, Progressive	C10.228.140.490.375.130.650; C10.228.140.490.493.063.650

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
dimethylselenide	increases expression, increases oxidation	1
fipronil	affects cotreatment, decreases expression	1
DEET	affects cotreatment, decreases expression	1
Ozone	increases expression, increases oxidation	1
Hydroxyl Radical	increases expression, increases oxidation	1

Clinical trials (associated diseases)

3 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00006191	Not specified	COMPLETED	Effect of Levetiracetam on Brain Excitability
NCT06593951	Not specified	RECRUITING	Registry and Natural History Study for Progressive Myoclonus Epilepsy Type 1 (EPM1)
NCT06923241	Not specified	COMPLETED	Nutri-score Labelling in a UK Restaurant Setting: a Randomised Control Trial