PJA1

gene
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Also known as FLJ11830RNF70PRAJA1

Summary

PJA1 (praja ring finger ubiquitin ligase 1, HGNC:16648) is a protein-coding gene on chromosome Xq13.1, encoding E3 ubiquitin-protein ligase Praja-1 (Q8NG27). Has E2-dependent E3 ubiquitin-protein ligase activity.

This gene encodes an enzyme that has E2-dependent E3 ubiquitin-protein ligase activity. This enzyme belongs to a class of ubiquitin ligases that include a RING finger motif, and it can interact with the E2 ubiquitin-conjugating enzyme UbcH5B. This gene is located in an area of chromosome X where several X-linked cognitive disability disorders have been associated, and it has also been found as part of a contiguous gene deletion associated with craniofrontonasal syndrome, though a direct link to any disorder has yet to be demonstrated. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 64219 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): X-linked complex neurodevelopmental disorder (Moderate, GenCC)
  • GWAS associations: 6
  • Clinical variants (ClinVar): 96 total
  • MANE Select transcript: NM_001032396

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16648
Approved symbolPJA1
Namepraja ring finger ubiquitin ligase 1
LocationXq13.1
Locus typegene with protein product
StatusApproved
AliasesFLJ11830, RNF70, PRAJA1
Ensembl geneENSG00000181191
Ensembl biotypeprotein_coding
OMIM300420
Entrez64219

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000361478, ENST00000374571, ENST00000374583, ENST00000374584, ENST00000471141, ENST00000477231, ENST00000590146, ENST00000901511

RefSeq mRNA: 5 — MANE Select: NM_001032396 NM_001032396, NM_001382775, NM_001382776, NM_022368, NM_145119

CCDS: CCDS14392, CCDS14393, CCDS35316

Canonical transcript exons

ENST00000374571 — 2 exons

ExonStartEnd
ENSE000014638486916086169163140
ENSE000028941786916537269165453

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 97.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.7009 / max 364.7686, expressed in 1757 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
19952314.38631750
1995241.3146724

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534397.93gold quality
ganglionic eminenceUBERON:000402397.63gold quality
corpus epididymisUBERON:000435997.46gold quality
ventricular zoneUBERON:000305397.20gold quality
embryoUBERON:000092296.11gold quality
nucleus accumbensUBERON:000188295.20gold quality
middle temporal gyrusUBERON:000277194.30gold quality
anterior cingulate cortexUBERON:000983594.09gold quality
cingulate cortexUBERON:000302794.01gold quality
dorsolateral prefrontal cortexUBERON:000983493.91gold quality
prefrontal cortexUBERON:000045193.62gold quality
Brodmann (1909) area 9UBERON:001354093.59gold quality
caudate nucleusUBERON:000187393.42gold quality
hypothalamusUBERON:000189893.33gold quality
neocortexUBERON:000195092.98gold quality
islet of LangerhansUBERON:000000692.96gold quality
putamenUBERON:000187492.78gold quality
right frontal lobeUBERON:000281092.78gold quality
frontal cortexUBERON:000187092.67gold quality
cerebral cortexUBERON:000095692.63gold quality
amygdalaUBERON:000187692.61gold quality
telencephalonUBERON:000189392.56gold quality
forebrainUBERON:000189092.24gold quality
brainUBERON:000095591.49gold quality
temporal lobeUBERON:000187191.31gold quality
Brodmann (1909) area 46UBERON:000648391.02gold quality
Ammon’s hornUBERON:000195491.00gold quality
adenohypophysisUBERON:000219690.54gold quality
cerebellar vermisUBERON:000472090.12gold quality
superior frontal gyrusUBERON:000266189.93gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.08

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYOD1

miRNA regulators (miRDB)

35 targeting PJA1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-340-5P100.0072.504437
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-211099.9666.681930
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-205-3P99.9269.923165
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-313399.8170.923506
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-431099.5968.842527
HSA-MIR-205399.5769.151635
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-17-3P99.5566.771311
HSA-MIR-105-5P99.5469.242060
HSA-MIR-7853-5P99.5469.302055
HSA-MIR-208A-5P99.4270.831913
HSA-MIR-208B-5P99.4270.831952
HSA-MIR-100-3P99.2067.33672
HSA-MIR-4520-2-3P99.1469.281009
HSA-MIR-475298.7168.04833
HSA-MIR-7850-5P98.1267.281111
HSA-MIR-509-3P98.1267.25612
HSA-MIR-876-5P97.9968.491345
HSA-MIR-5088-5P97.9764.28487
HSA-MIR-427597.9668.421549

Literature-anchored findings (GeneRIF, showing 10)

  • A RING finger protein Praja1 regulates Dlx5-dependent transcription through its ubiquitin ligase activity for the Dlx/Msx-interacting MAGE/Necdin family protein, Dlxin-1. (PMID:11959851)
  • Involved in protein ubiquitination in the brain. Candidate gene for X-linked mental retardation. (PMID:12036302)
  • Data provide clues into novel aspects of Praja1 function. (PMID:21461837)
  • these results suggest a role for PRAJA1 in regulating the level of PRC2 by targeting its free subunits for Ub-mediated proteasomal degradation. (PMID:21513699)
  • Targeting the E3 Ubiquitin Ligase PJA1 Enhances Tumor-Suppressing TGFbeta Signaling. (PMID:32127355)
  • A recurrent PJA1 variant in trigonocephaly and neurodevelopmental disorders. (PMID:32530565)
  • Praja1 RING-finger E3 ubiquitin ligase suppresses neuronal cytoplasmic TDP-43 aggregate formation. (PMID:32686212)
  • E3 ubiquitin ligase PJA1 regulates lung adenocarcinoma apoptosis and invasion through promoting FOXR2 degradation. (PMID:33839405)
  • Praja1 ubiquitin ligase facilitates degradation of polyglutamine proteins and suppresses polyglutamine-mediated toxicity. (PMID:34161122)
  • PJA1-mediated suppression of pyroptosis as a driver of docetaxel resistance in nasopharyngeal carcinoma. (PMID:38906860)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriopja2ENSDARG00000100296
mus_musculusPja1ENSMUSG00000034403
rattus_norvegicusPja1ENSRNOG00000047339

Paralogs (1): PJA2 (ENSG00000198961)

Protein

Protein identifiers

E3 ubiquitin-protein ligase Praja-1Q8NG27 (reviewed: Q8NG27)

Alternative names: RING finger protein 70, RING-type E3 ubiquitin transferase Praja-1

All UniProt accessions (3): Q8NG27, K7EPI8, K7EPW5

UniProt curated annotations — full annotation on UniProt →

Function. Has E2-dependent E3 ubiquitin-protein ligase activity. Ubiquitinates MAGED1 antigen leading to its subsequent degradation by proteasome. May be involved in protein sorting.

Subunit / interactions. Binds ubiquitin-conjugating enzymes (E2s). In vitro, interacts with the ubiquitin-conjugating enzyme, UBE2D2.

Tissue specificity. Expressed in various regions of the brain including the cerebellum, cerebral cortex, medulla, occipital pole, frontal lobe, temporal lobe and putamen. Highest levels in the cerebral cortex.

Post-translational modifications. Substrate for E2-dependent ubiquitination.

Domain organisation. The RING-type zinc finger domain interacts with an ubiquitin-conjugating enzyme (E2) and facilitates ubiquitination.

Miscellaneous. PubMed:12036302 reported that isoform 2 arises by alternative initiation.

Isoforms (3)

UniProt IDNamesCanonical?
Q8NG27-11yes
Q8NG27-22, PJA1-beta, Praja1-beta
Q8NG27-33

RefSeq proteins (5): NP_001027568, NP_001369704, NP_001369705, NP_071763, NP_660095 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily

Pfam: PF13639

UniProt features (30 total): compositionally biased region 8, strand 5, modified residue 4, turn 3, splice variant 2, sequence variant 2, region of interest 2, helix 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2L0BSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NG27-F150.150.07

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 265, 277, 365, 367

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation

MSigDB gene sets: 149 (showing top): REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGGTGGRR_PAX4_03, MARTINEZ_RB1_TARGETS_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, HP1SITEFACTOR_Q6, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, EGR1_01, BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN, GOBP_PROTEIN_CATABOLIC_PROCESS, TAATTA_CHX10_01, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (2): protein ubiquitination (GO:0016567), protein catabolic process (GO:0030163)

GO Molecular Function (5): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (1): cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Class I MHC mediated antigen processing & presentation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein modification by small protein conjugation1
macromolecule catabolic process1
protein metabolic process1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

840 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PJA1MAGED1Q9Y5V3992
PJA1OPHN1O60890828
PJA1NDNQ99608789
PJA1EFNB1P98172715
PJA1UBE2D2P51669639
PJA1MAGEA1P43355515
PJA1MAGEB18Q96M61417
PJA1NSMCE3Q96MG7406
PJA1SMURF2Q9HAU4388
PJA1EPHB1P54762386
PJA1GINM1Q9NU53363
PJA1EPHB4P54760360
PJA1YIPF6Q96EC8327
PJA1MAGEF1Q9HAY2324
PJA1SMC5Q8IY18322

IntAct

60 interactions, top by confidence:

ABTypeScore
PJA1MAGED1psi-mi:“MI:0915”(physical association)0.740
MAGED1PJA1psi-mi:“MI:0915”(physical association)0.740
MAGED1PJA1psi-mi:“MI:0403”(colocalization)0.740
NSMCE3PJA1psi-mi:“MI:0914”(association)0.710
NSMCE3PJA1psi-mi:“MI:0915”(physical association)0.710
PJA1SMC5psi-mi:“MI:0914”(association)0.530
SKP2DPYSL4psi-mi:“MI:0914”(association)0.530
CPA6PPM1Gpsi-mi:“MI:0914”(association)0.530
LRRC27HMOX1psi-mi:“MI:0914”(association)0.530
SPSB2ARHGEF10psi-mi:“MI:0914”(association)0.530
SPSB4ARHGEF10psi-mi:“MI:0914”(association)0.530
SMAD3FAM83Gpsi-mi:“MI:0915”(physical association)0.400
PJA1UBE2Upsi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
AP2M1C1orf226psi-mi:“MI:0914”(association)0.350
IQCNTARSL2psi-mi:“MI:0914”(association)0.350
HNRNPLLTBX3psi-mi:“MI:0914”(association)0.350
DOCK5DPYSL4psi-mi:“MI:0914”(association)0.350
LRRC27HMOX1psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
ARRDC2ZSWIM8psi-mi:“MI:0914”(association)0.350
TXNIPZSWIM8psi-mi:“MI:0914”(association)0.350
MYO9BPPM1Gpsi-mi:“MI:0914”(association)0.350
FBXO10BLTP3Bpsi-mi:“MI:0914”(association)0.350
IQCNTARS3psi-mi:“MI:0914”(association)0.350
DUSP16MEIOCpsi-mi:“MI:0914”(association)0.350

BioGRID (179): PJA1 (Biochemical Activity), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), PJA1 (Proximity Label-MS), PJA1 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LFM6, A0A1B0GVH6, A1A4G5, A1CQN6, A7A241, A9RNY0, B0QZF7, B9UYK6, E9Q309, H0WFA5, O23372, O35413, O94875, P02686, P43587, Q0VFP3, Q0WL69, Q12912, Q17QQ9, Q1G3K8, Q32KY7, Q3UTJ2, Q499E5, Q4R309, Q4R881, Q4V7T5, Q56WM6, Q5E9A0, Q5PPL1, Q5R6I3, Q5VT06, Q62417, Q6AYU0, Q6DD19, Q6GP48, Q6H7U2, Q8K2H1, Q8L4M6, Q8NEY8, Q8NG27

Diamond homologs: A5WWA0, A8Y4B2, E9QAU8, O00237, O22197, O22283, O43085, O54965, O55176, O64763, P0CH03, P0CH30, P0DPR2, P87119, P90859, Q08CG8, Q08D68, Q0II22, Q2KHN1, Q3T0W3, Q3U2C5, Q3UHJ8, Q4KLR8, Q4V7B8, Q566M8, Q5DTZ6, Q5M974, Q5QLR5, Q5RBT7, Q5SPX3, Q5SSZ7, Q5XHH7, Q66HG0, Q6AXU4, Q6DIP3, Q6GPV5, Q6IRP0, Q6NPT7, Q6NRL6, Q6NRX0

SIGNOR signaling

5 interactions.

AEffectBMechanism
PJA1down-regulatesSPTBN1ubiquitination
Ub:E2“up-regulates activity”PJA1ubiquitination
PJA1“down-regulates activity”SMAD3ubiquitination
PJA1“down-regulates quantity by destabilization”EZH2ubiquitination
MYOD1“up-regulates quantity”PJA1“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance53
Likely benign14
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

22 predictions. Top by Δscore:

VariantEffectΔscore
X:69163421:T:Adonor_gain0.8900
X:69163501:CAAGA:Cdonor_gain0.3500
X:69162382:C:CAacceptor_gain0.3400
X:69163428:AGG:Adonor_gain0.3300
X:69162383:T:Aacceptor_gain0.3100
X:69163497:A:ACdonor_gain0.3000
X:69162382:C:CCacceptor_gain0.2800
X:69162381:ACTGT:Aacceptor_gain0.2600
X:69163418:CTTT:Cdonor_gain0.2500
X:69163531:A:ACdonor_gain0.2400
X:69162381:A:ACacceptor_gain0.2300
X:69163417:A:ACdonor_gain0.2300
X:69163418:C:CCdonor_gain0.2300
X:69162408:A:Tacceptor_gain0.2200
X:69163419:T:Cdonor_gain0.2200
X:69161891:G:GAacceptor_gain0.2100
X:69161892:A:AAacceptor_gain0.2100
X:69161893:A:AAacceptor_gain0.2100
X:69163427:AAGG:Adonor_gain0.2100
X:69162526:A:ACdonor_gain0.2000
X:69162527:C:CCdonor_gain0.2000
X:69162747:TGGCC:Tacceptor_gain0.2000

AlphaMissense

3899 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:69161335:C:TC635Y1.000
X:69161336:A:GC635R1.000
X:69161343:G:CC632W1.000
X:69161344:C:TC632Y1.000
X:69161345:A:GC632R1.000
X:69161362:A:GL626P1.000
X:69161364:C:AW625C1.000
X:69161364:C:GW625C1.000
X:69161366:A:GW625R1.000
X:69161366:A:TW625R1.000
X:69161376:A:CC621W1.000
X:69161377:C:TC621Y1.000
X:69161378:A:GC621R1.000
X:69161388:G:CF617L1.000
X:69161388:G:TF617L1.000
X:69161389:A:GF617S1.000
X:69161390:A:GF617L1.000
X:69161401:C:TC613Y1.000
X:69161402:A:GC613R1.000
X:69161407:A:GL611P1.000
X:69161445:G:CC598W1.000
X:69161446:C:TC598Y1.000
X:69161447:A:GC598R1.000
X:69161454:G:CC595W1.000
X:69161455:C:TC595Y1.000
X:69161456:A:GC595R1.000
X:69161575:A:GL555S1.000
X:69161584:A:GL552P1.000
X:69161587:G:TA551D1.000
X:69161600:C:GA547P1.000

dbSNP variants (sampled 300 via entrez): RS1001541505 (X:69162046 C>A,T), RS1001855452 (X:69167006 A>G), RS1002169974 (X:69166742 C>T), RS1002723963 (X:69165265 C>G,T), RS1002860071 (X:69165507 G>A), RS1003315706 (X:69163221 G>T), RS1003958091 (X:69163244 T>C), RS1004027372 (X:69165710 G>GT), RS1004275192 (X:69164640 G>T), RS1005211585 (X:69167337 T>A), RS1006043710 (X:69160401 T>G), RS1006404444 (X:69160349 A>C), RS1006767177 (X:69161777 C>A,G), RS1007814469 (X:69166471 A>C), RS1008138395 (X:69163780 A>T)

Disease associations

OMIM: gene MIM:300420 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
X-linked complex neurodevelopmental disorderModerateX-linked

Mondo (1): X-linked complex neurodevelopmental disorder (MONDO:0100148)

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002539_98Schizophrenia2.000000e-10
GCST006803_26Schizophrenia1.000000e-12
GCST008129_36Body mass index2.000000e-10
GCST008362_133Birth weight4.000000e-10
GCST90002400_2Plateletcrit5.000000e-12
GCST90002402_515Platelet count3.000000e-14

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0004344birth weight
EFO:0007985platelet crit
EFO:0004309platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
beta-lapachoneincreases expression1
sodium arseniteincreases expression1
manganese chlorideincreases abundance, increases expression1
coumarinincreases phosphorylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
Decitabineincreases expression1
Sunitinibdecreases expression1
Azacitidineincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cisplatinincreases expression1
Doxorubicindecreases expression1
Manganeseincreases abundance, increases expression1
Methyl Methanesulfonateincreases expression1
Seleniumincreases expression1
Tretinoindecreases expression1
Valproic Acidincreases expression1
Vitamin Eincreases expression1
Cyclosporineincreases expression1
Aflatoxin B1decreases methylation1
Antirheumatic Agentsincreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E2GTHAP1 PJA1 (-)Cancer cell lineMale

Clinical trials (associated diseases)

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