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PRICKLE3 prickle planar cell polarity protein 3 [ Homo sapiens (human) ]

Gene ID: 4007, updated on 2-Nov-2024

Summary

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Official Symbol
PRICKLE3provided by HGNC
Official Full Name
prickle planar cell polarity protein 3provided by HGNC
Primary source
HGNC:HGNC:6645
See related
Ensembl:ENSG00000012211 MIM:300111; AllianceGenome:HGNC:6645
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Pk3; LMO6; LOAM; LOAS
Summary
LIM domain only 6 is a three LIM domain-containing protein. The LIM domain is a cysteine-rich sequence motif that binds zinc atoms to form a specific protein-binding interface for protein-protein interactions. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in skin (RPKM 16.7), esophagus (RPKM 11.7) and 24 other tissues See more
Orthologs
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Genomic context

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See PRICKLE3 in Genome Data Viewer
Location:
Xp11.23
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (49174802..49186373, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48586552..48598227, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49031151..49042826, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373195 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 1 Neighboring gene RNA, 7SL, cytoplasmic 262, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49019052-49019751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20837 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49022309-49023254 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 10 Neighboring gene MAGI family member, X-linked Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20838 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49032849-49033350 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 11 Neighboring gene proteolipid protein 2 Neighboring gene CRISPRi-FlowFISH-validated GATA1 and PLP2 regulatory element Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29635 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 13 Neighboring gene synaptophysin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20843 Neighboring gene SYP antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:49065732-49066931 Neighboring gene calcium voltage-gated channel subunit alpha1 F Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:49086994-49087652

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. PRICKLE3 linked to ATPase biogenesis manifested Leber's hereditary optic neuropathy. Yu J, et al. J Clin Invest, 2020 Sep 1. PMID 32516135, Free PMC Article
  2. Sequence-based exon prediction around the synaptophysin locus reveals a gene-rich area containing novel genes in human proximal Xp. Fisher SE, et al. Genomics, 1997 Oct 15. PMID 9344658
  3. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Hauri S, et al. Mol Syst Biol, 2013. PMID 24366813, Free PMC Article
  4. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. Wu C, et al. Proteomics, 2007 Jun. PMID 17474147
  5. HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways. Monda JK, et al. Cell Rep, 2023 May 30. PMID 37167062, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PRICKLE3 linked to ATPase biogenesis manifested Leber's hereditary optic neuropathy.
    Title: PRICKLE3 linked to ATPase biogenesis manifested Leber's hereditary optic neuropathy.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Leber optic atrophy, susceptibility to
MedGen: C1839891 OMIM: 308905 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in cell projection organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
prickle planar cell polarity protein 3
Names
LIM domain only protein 6
LMO-6
prickle homolog 3
prickle-like protein 3
triple LIM domain protein 6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_017135.2 RefSeqGene

    Range
    5000..16571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001307979.2 → NP_001294908.1  prickle planar cell polarity protein 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate 5' exon, contains an alternate 5' terminal exon, and uses a downstream start codon, compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AA524273, AK299407, AK303200, BM981706, DC407811
    Consensus CDS
    CCDS78481.1
    UniProtKB/TrEMBL
    B7Z8D2, H0Y413
    Related
    ENSP00000388599.2, ENST00000453382.5
    Conserved Domains (4) summary
    cd09415
    Location:118 → 176
    LIM1_Prickle; The first LIM domain of Prickle
    cd09418
    Location:181 → 236
    LIM2_Prickle; The second LIM domain of Prickle
    cd09420
    Location:241 → 299
    LIM3_Prickle; The third LIM domain of Prickle
    cd09827
    Location:14 → 110
    PET_Prickle; The PET domain of Prickle

  2. NM_006150.5 → NP_006141.2  prickle planar cell polarity protein 3 isoform 1

    See identical proteins and their annotated locations for NP_006141.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA524273, AK299407, AK303200, BC002468, BC016856, BM981706, BP227957
    Consensus CDS
    CCDS14320.1
    UniProtKB/Swiss-Prot
    B7Z8F2, O43900, O76007, Q53XR5
    UniProtKB/TrEMBL
    B2RBS3, Q6IAE4
    Related
    ENSP00000470248.1, ENST00000599218.6
    Conserved Domains (4) summary
    cd09415
    Location:186 → 244
    LIM1_Prickle; The first LIM domain of Prickle
    cd09418
    Location:249 → 304
    LIM2_Prickle; The second LIM domain of Prickle
    cd09420
    Location:309 → 367
    LIM3_Prickle; The third LIM domain of Prickle
    cd09827
    Location:82 → 178
    PET_Prickle; The PET domain of Prickle

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    49174802..49186373 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    48586552..48598227 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43900.2 GenPept UniProtKB/Swiss-Prot:O43900

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