PAK1IP1

gene
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Also known as FLJ20624hPIP1PIP1bA421M1.5MAK11WDR84

Summary

PAK1IP1 (PAK1 interacting protein 1, HGNC:20882) is a protein-coding gene on chromosome 6p24.2, encoding p21-activated protein kinase-interacting protein 1 (Q9NWT1). Negatively regulates the PAK1 kinase. It is a common-essential gene (DepMap: required in 98.4% of cancer cell lines).

Predicted to enable protein kinase inhibitor activity. Involved in regulation of signal transduction by p53 class mediator and ribosomal large subunit biogenesis. Located in nucleolus.

Source: NCBI Gene 55003 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 63 total
  • Cancer dependency (DepMap): dependent in 98.4% of screened cell lines (common-essential)
  • MANE Select transcript: NM_017906

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20882
Approved symbolPAK1IP1
NamePAK1 interacting protein 1
Location6p24.2
Locus typegene with protein product
StatusApproved
AliasesFLJ20624, hPIP1, PIP1, bA421M1.5, MAK11, WDR84
Ensembl geneENSG00000111845
Ensembl biotypeprotein_coding
OMIM607811
Entrez55003

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000379568, ENST00000896220, ENST00000930921, ENST00000930922, ENST00000930923, ENST00000930924, ENST00000930925, ENST00000930926, ENST00000930927, ENST00000966254

RefSeq mRNA: 1 — MANE Select: NM_017906 NM_017906

CCDS: CCDS34339

Canonical transcript exons

ENST00000379568 — 10 exons

ExonStartEnd
ENSE000006157761070236910702489
ENSE000006845511070895310709076
ENSE000006845541070741510707514
ENSE000006845561070474710704844
ENSE000006845591070450710704652
ENSE000006845621070340510703457
ENSE000006845641070256510702639
ENSE000008480001069732410697486
ENSE000014816111070923810709782
ENSE000014816611069497210695069

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.6153 / max 310.2371, expressed in 1813 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
6577633.14811813
657750.4672244

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
prostate glandUBERON:000236791.49gold quality
calcaneal tendonUBERON:000370190.09gold quality
endometriumUBERON:000129589.96gold quality
cortical plateUBERON:000534389.26gold quality
islet of LangerhansUBERON:000000688.52gold quality
esophagus mucosaUBERON:000246987.83gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.77gold quality
smooth muscle tissueUBERON:000113587.44gold quality
gastrocnemiusUBERON:000138886.67gold quality
muscle of legUBERON:000138386.21gold quality
monocyteCL:000057686.18gold quality
leukocyteCL:000073885.84gold quality
rectumUBERON:000105285.67gold quality
vermiform appendixUBERON:000115485.55gold quality
omental fat padUBERON:001041485.47gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.31gold quality
esophagusUBERON:000104385.24gold quality
mucosa of transverse colonUBERON:000499185.15gold quality
placentaUBERON:000198785.12gold quality
pancreasUBERON:000126484.94gold quality
tibial nerveUBERON:000132384.60gold quality
left adrenal glandUBERON:000123484.56gold quality
left uterine tubeUBERON:000130384.54gold quality
adrenal glandUBERON:000236984.47gold quality
adipose tissueUBERON:000101384.41gold quality
lymph nodeUBERON:000002984.34gold quality
muscle tissueUBERON:000238584.30gold quality
left adrenal gland cortexUBERON:003582584.27gold quality
tonsilUBERON:000237284.07gold quality
corpus callosumUBERON:000233683.96gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting PAK1IP1, 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-5011-5P100.0083.465820
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-590-3P99.9674.346478
HSA-LET-7C-3P99.9573.422862
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • A mutation in mouse Pak1ip1 causes orofacial clefting while human PAK1IP1 maps to 6p24 translocation breaking points associated with orofacial clefting. (PMID:23935987)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriopak1ip1ENSDARG00000044488
mus_musculusPak1ip1ENSMUSG00000038683
rattus_norvegicusTmem14cENSRNOG00000015437
drosophila_melanogasterCG12608FBGN0030630

Paralogs (26): PAFAH1B1 (ENSG00000007168), SNRNP40 (ENSG00000060688), WDR62 (ENSG00000075702), WDR7 (ENSG00000091157), TBL2 (ENSG00000106638), WDR75 (ENSG00000115368), DCAF4 (ENSG00000119599), DAW1 (ENSG00000123977), TEP1 (ENSG00000129566), AHI1 (ENSG00000135541), WDR38 (ENSG00000136918), MAPKBP1 (ENSG00000137802), POC1B (ENSG00000139323), NEDD1 (ENSG00000139350), COP1 (ENSG00000143207), WDR17 (ENSG00000150627), WDR43 (ENSG00000163811), POC1A (ENSG00000164087), WDR88 (ENSG00000166359), WDR81 (ENSG00000167716), DCAF4L2 (ENSG00000176566), DCAF4L1 (ENSG00000182308), WDR27 (ENSG00000184465), NWD1 (ENSG00000188039), WDR5 (ENSG00000196363), WDR5B (ENSG00000196981)

Protein

Protein identifiers

p21-activated protein kinase-interacting protein 1Q9NWT1 (reviewed: Q9NWT1)

Alternative names: PAK/PLC-interacting protein 1, PAK1-interacting protein 1, WD repeat-containing protein 84

All UniProt accessions (2): Q9NWT1, A0A0S2Z5C3

UniProt curated annotations — full annotation on UniProt →

Function. Negatively regulates the PAK1 kinase. PAK1 is a member of the PAK kinase family, which has been shown to play a positive role in the regulation of signaling pathways involving MAPK8 and RELA. PAK1 exists as an inactive homodimer, which is activated by binding of small GTPases such as CDC42 to an N-terminal regulatory domain. PAK1IP1 also binds to the N-terminus of PAK1, and inhibits the specific activation of PAK1 by CDC42. May be involved in ribosomal large subunit assembly.

Subunit / interactions. Interacts with PAK1.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Expressed in brain, colon, heart, kidney, liver, lung, muscle, peripheral blood leukocytes, placenta, small intestine, spleen and thymus.

RefSeq proteins (1): NP_060376* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR020472WD40_PAC1Repeat
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR051959PAK1-Kinase_RegulatorFamily

Pfam: PF00400

UniProt features (18 total): sequence conflict 7, repeat 6, compositionally biased region 2, chain 1, modified residue 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NWT1-F181.270.69

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 (1): 320

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 165 (showing top): GOBP_RIBOSOME_BIOGENESIS, MULLIGHAN_NPM1_SIGNATURE_3_UP, chr6p24, LFA1_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MODULE_453, PAX8_B, NKX62_Q2, MODULE_256, GOBP_MATURATION_OF_LSU_RRNA, WTGAAAT_UNKNOWN, HNF4_DR1_Q3, PPAR_DR1_Q2, GARY_CD5_TARGETS_DN, HTF_01

GO Biological Process (7): maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000463), cell population proliferation (GO:0008283), negative regulation of signal transduction (GO:0009968), ribosomal large subunit biogenesis (GO:0042273), roof of mouth development (GO:0060021), regulation of signal transduction by p53 class mediator (GO:1901796), ribosome biogenesis (GO:0042254)

GO Molecular Function (2): protein kinase inhibitor activity (GO:0004860), protein binding (GO:0005515)

GO Cellular Component (2): nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ribonucleoprotein complex biogenesis2
maturation of LSU-rRNA1
cellular process1
signal transduction1
regulation of signal transduction1
negative regulation of cell communication1
negative regulation of signaling1
negative regulation of response to stimulus1
ribosome biogenesis1
anatomical structure development1
signal transduction by p53 class mediator1
regulation of intracellular signal transduction1
protein kinase activity1
kinase inhibitor activity1
protein kinase regulator activity1
binding1
nuclear lumen1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1966 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PAK1IP1RSL24D1Q9UHA3841
PAK1IP1NSA2O95478744
PAK1IP1RPF2Q9H7B2740
PAK1IP1PDCD11Q14690718
PAK1IP1NIP7Q9Y221716
PAK1IP1RRP15Q9Y3B9696
PAK1IP1GNL2Q13823682
PAK1IP1GTPBP4Q9BZE4647
PAK1IP1NOP2P46087630
PAK1IP1CDC40O60508617
PAK1IP1HTATSF1O43719605
PAK1IP1NCK1P16333604
PAK1IP1WDR12Q9GZL7601
PAK1IP1SURF6O75683583
PAK1IP1EBNA1BP2Q99848576

IntAct

131 interactions, top by confidence:

ABTypeScore
PAK1IP1MEOX2psi-mi:“MI:0915”(physical association)0.720
MEOX2PAK1IP1psi-mi:“MI:0915”(physical association)0.720
KPNA1TCERG1psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
PLEKHF2PAK1IP1psi-mi:“MI:0915”(physical association)0.560
RPL28MAGEB2psi-mi:“MI:0914”(association)0.560
RBM34NVLpsi-mi:“MI:0914”(association)0.530
H1-4IGF2BP3psi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
ZNF2MPHOSPH10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
PPANPPM1Gpsi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
ZNF71DKC1psi-mi:“MI:0914”(association)0.530
RPL7ANVLpsi-mi:“MI:0914”(association)0.530
Ruvbl1AAR2psi-mi:“MI:0914”(association)0.350
RPL10RPS6psi-mi:“MI:0914”(association)0.350
Srp72psi-mi:“MI:0914”(association)0.350
RRP1BZNF785psi-mi:“MI:0914”(association)0.350
MKI67ARHGAP10psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (161): PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Co-fractionation), PAK1IP1 (Co-fractionation), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS), PAK1IP1 (Affinity Capture-MS)

ESM2 similar proteins: A4D1P6, A4IGH4, A7E3S5, A7UVN1, B0W8M5, B2RYI0, B3MRC6, B3NXQ7, B4GXH4, B4JWS7, B4L6T9, B4MA12, B4NER4, B4PYR0, B5DMC9, O74453, O74863, O95163, P57081, Q17CH9, Q2TAF3, Q3TIU4, Q3UMY5, Q4KLQ5, Q5EA99, Q5FVB6, Q5ZKU8, Q5ZLL7, Q68FJ6, Q6C953, Q6DIP5, Q6TEN6, Q6TNS2, Q750U8, Q7TMQ7, Q7TT37, Q7ZVR1, Q7ZY78, Q8BUI3, Q8BX17

Diamond homologs: Q5EA99, Q5ZKU8, Q68FJ6, Q6TNS2, Q9DCE5, Q9NWT1, A0CH87, A0DB19, A0JPH4, A1CF18, A1CQI9, A1CUD6, A1DDL6, A1DP19, A2RRU4, A4R3M4, A4RJV3, A6QM06, A6QX61, A7EKM8, B0XM00, B2B766, B6HP56, B6QC06, B6QC56, B8N9H4, C0NRC6, C4JPW9, C5PFX0, C6HTE8, D1ZEB4, D1ZEM6, D5GBI7, G4MQX3, P83774, P97260, Q00664, Q01369, Q0CCP0, Q0CJD8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 135 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Peptide chain elongation2839.0×3e-36
Viral mRNA Translation2839.0×3e-36
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA2838.6×3e-36
Selenocysteine synthesis2837.0×7e-36
Eukaryotic Translation Termination2837.0×7e-36
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)2836.2×1e-35
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA2836.2×1e-35
Formation of a pool of free 40S subunits2834.5×4e-35

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation2944.0×4e-38
translation2924.4×4e-30
ribosomal large subunit biogenesis621.8×3e-05
rRNA processing1416.2×3e-11
ribosomal small subunit biogenesis814.9×8e-06
regulation of alternative mRNA splicing, via spliceosome714.0×5e-05
negative regulation of translation812.8×2e-05
RNA processing712.6×7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance39
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1225 predictions. Top by Δscore:

VariantEffectΔscore
6:10697484:GTG:Gdonor_gain1.0000
6:10702485:CACAA:Cdonor_gain1.0000
6:10702486:ACAA:Adonor_gain1.0000
6:10702486:ACAAG:Adonor_loss1.0000
6:10702487:CAA:Cdonor_gain1.0000
6:10702487:CAAG:Cdonor_loss1.0000
6:10702488:AA:Adonor_gain1.0000
6:10702489:AG:Adonor_loss1.0000
6:10702490:G:Adonor_loss1.0000
6:10702490:G:GGdonor_gain1.0000
6:10702491:T:Adonor_loss1.0000
6:10702492:GA:Gdonor_loss1.0000
6:10704499:A:AGacceptor_gain1.0000
6:10704505:A:AGacceptor_gain1.0000
6:10704506:G:GTacceptor_gain1.0000
6:10704506:GAT:Gacceptor_gain1.0000
6:10704648:TTTCA:Tdonor_gain1.0000
6:10704649:TTCA:Tdonor_gain1.0000
6:10704650:TCA:Tdonor_gain1.0000
6:10704650:TCAG:Tdonor_loss1.0000
6:10704651:CA:Cdonor_gain1.0000
6:10704651:CAG:Cdonor_loss1.0000
6:10704652:AGT:Adonor_loss1.0000
6:10704653:G:GGdonor_gain1.0000
6:10704654:T:Adonor_loss1.0000
6:10704655:AAG:Adonor_loss1.0000
6:10704744:TAG:Tacceptor_loss1.0000
6:10704745:A:AGacceptor_gain1.0000
6:10704745:A:ATacceptor_loss1.0000
6:10704745:AG:Aacceptor_gain1.0000

AlphaMissense

2610 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:10702413:A:CS98R0.999
6:10702415:T:AS98R0.999
6:10702415:T:GS98R0.999
6:10703409:T:AW150R0.999
6:10703409:T:CW150R0.999
6:10704524:T:AW172R0.999
6:10704524:T:CW172R0.999
6:10702609:C:AA138D0.998
6:10702612:T:CL139P0.998
6:10702614:T:CS140P0.998
6:10702618:T:AV141D0.998
6:10697414:A:CS59R0.997
6:10697416:C:AS59R0.997
6:10697416:C:GS59R0.997
6:10702443:T:AW108R0.997
6:10702443:T:CW108R0.997
6:10702615:C:GS140W0.997
6:10703436:T:CF159L0.997
6:10703438:C:AF159L0.997
6:10703438:C:GF159L0.997
6:10697411:G:TG58W0.996
6:10697412:G:AG58E0.996
6:10697420:G:CD61H0.996
6:10702584:T:CS130P0.996
6:10702620:G:CG142R0.996
6:10702621:G:TG142V0.996
6:10702626:G:CD144H0.996
6:10702627:A:TD144V0.996
6:10704526:G:CW172C0.996
6:10704526:G:TW172C0.996

dbSNP variants (sampled 300 via entrez): RS1000038898 (6:10694166 AG>A), RS1001055212 (6:10704648 T>C), RS1001162607 (6:10698230 A>G), RS1001381326 (6:10707812 A>G), RS1001463349 (6:10695389 A>G), RS1001512278 (6:10698005 A>G), RS1001712315 (6:10693280 C>A,T), RS1002027843 (6:10691882 G>A), RS1002080127 (6:10692237 G>C,T), RS1002153952 (6:10692472 T>C), RS1002219891 (6:10708581 C>T), RS1002241269 (6:10702261 GAA>G,GA,GAAA), RS1002668895 (6:10697614 A>G,T), RS1002783555 (6:10709635 T>C), RS1002960331 (6:10709959 G>C)

Disease associations

OMIM: gene MIM:607811 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, affects expression, decreases expression3
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression2
Cyclosporineincreases expression2
Particulate Matterdecreases expression, increases abundance, increases expression, affects cotreatment2
FR900359decreases phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
deoxynivalenolincreases expression1
trichostatin Aaffects expression1
cobaltous chloridedecreases expression1
butyraldehydeincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
abrineincreases expression1
bisphenol Saffects expression1
jinfukangaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Caffeinedecreases phosphorylation1
Calcitriolincreases expression, affects cotreatment1
Cisplatinaffects cotreatment, decreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.