PIK3IP1

gene
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Also known as HGFLMGC17330TrIP

Summary

PIK3IP1 (phosphoinositide-3-kinase interacting protein 1, HGNC:24942) is a protein-coding gene on chromosome 22q12.2, encoding Phosphoinositide-3-kinase-interacting protein 1 (Q96FE7). Negative regulator of hepatic phosphatidylinositol 3-kinase (PI3K) activity.

Enables phosphatidylinositol 3-kinase inhibitor activity. Involved in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction. Predicted to be located in plasma membrane. Predicted to be active in extracellular space.

Source: NCBI Gene 113791 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 47 total
  • MANE Select transcript: NM_052880

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24942
Approved symbolPIK3IP1
Namephosphoinositide-3-kinase interacting protein 1
Location22q12.2
Locus typegene with protein product
StatusApproved
AliasesHGFL, MGC17330, TrIP
Ensembl geneENSG00000100100
Ensembl biotypeprotein_coding
OMIM619158
Entrez113791

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 3 retained_intron

ENST00000215912, ENST00000402249, ENST00000441972, ENST00000443175, ENST00000480654, ENST00000493034, ENST00000715258, ENST00000885856

RefSeq mRNA: 2 — MANE Select: NM_052880 NM_001135911, NM_052880

CCDS: CCDS13893, CCDS46690

Canonical transcript exons

ENST00000215912 — 6 exons

ExonStartEnd
ENSE000006531443129096531291084
ENSE000006531493129118031291296
ENSE000010486933129227531292488
ENSE000018573583128160031283288
ENSE000035212813128931531289393
ENSE000036443203128949931289699

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 96.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.6229 / max 1642.0285, expressed in 1622 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter IDTPM avgSamples expressed
19369624.85631547
1936912.0334288
1936941.3843275
1936921.3640261
1936900.8441118
1936950.6894218
1936970.6354361
1936890.4992100
1936870.125546
1936880.101940

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lymph nodeUBERON:000002996.31gold quality
olfactory segment of nasal mucosaUBERON:000538696.16gold quality
right lungUBERON:000216796.12gold quality
granulocyteCL:000009495.35gold quality
bloodUBERON:000017895.12gold quality
mucosa of stomachUBERON:000119994.84gold quality
spleenUBERON:000210694.75gold quality
nerveUBERON:000102194.34gold quality
tibial nerveUBERON:000132394.34gold quality
skin of legUBERON:000151194.19gold quality
skin of abdomenUBERON:000141693.85gold quality
small intestine Peyer’s patchUBERON:000345493.75gold quality
minor salivary glandUBERON:000183093.59gold quality
vermiform appendixUBERON:000115493.50gold quality
pancreatic ductal cellCL:000207993.41gold quality
subcutaneous adipose tissueUBERON:000219092.80gold quality
calcaneal tendonUBERON:000370192.76gold quality
saliva-secreting glandUBERON:000104492.64gold quality
zone of skinUBERON:000001492.44gold quality
right coronary arteryUBERON:000162592.26gold quality
C1 segment of cervical spinal cordUBERON:000646992.25gold quality
caecumUBERON:000115392.04gold quality
right adrenal gland cortexUBERON:003582791.93gold quality
right adrenal glandUBERON:000123391.89gold quality
gall bladderUBERON:000211091.83gold quality
upper lobe of left lungUBERON:000895291.47gold quality
nasal cavity epitheliumUBERON:000538491.44gold quality
spinal cordUBERON:000224091.38gold quality
left adrenal glandUBERON:000123491.35gold quality
small intestineUBERON:000210891.24gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-HCAD-4yes669.22
E-MTAB-9467yes66.95
E-CURD-122yes39.95
E-CURD-88yes38.81
E-MTAB-8410yes36.62
E-HCAD-1yes36.39
E-CURD-112yes5.24
E-MTAB-7606no2613.73
E-CURD-89no1285.56
E-GEOD-150728no586.14
E-CURD-120no567.60
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CUX1, FOXO3

miRNA regulators (miRDB)

68 targeting PIK3IP1, 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-3163100.0077.238605
HSA-MIR-188-3P100.0068.761240
HSA-MIR-574-5P100.0066.01989
HSA-MIR-450099.9972.722367
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-302E99.9670.742669
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-552-5P99.9368.561583
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-539-5P99.9370.302855
HSA-MIR-497-5P99.9271.832674
HSA-MIR-429599.9073.111838
HSA-MIR-202-3P99.8471.411290

Literature-anchored findings (GeneRIF, showing 8)

  • PIK3IP1 directly binds to the p110 catalytic subunit and down modulates PI3K activity. Suggested that PIK3IP1 is a new type of PI3K regulator. (PMID:17475214)
  • PIK3IP1 is an important regulator of PI3K in vivo, and its dysregulation can contribute to liver carcinogenesis (PMID:18632611)
  • PIK3IP1-v1 is a novel splicing isoform of PIK3IP1. Both of them are located on cell membrane and can induce cell apoptosis. (PMID:19088825)
  • These results suggest that the novel PI3K regulator PIK3IP1 plays an inhibitory role in T-cell activation. (PMID:22706993)
  • Findings indicate that colon cancer associated transcript 1 (non-protein coding) (CCAT1) was upregulated in osteosarcoma tissues and cells, and was involved in the proliferation and migration of osteosarcoma via regulating miR-148a/phosphatidyl inositol 3-kinase interacting protein 1 (PIK3IP1) signal pathway. (PMID:28549102)
  • Pik3ip1 Is a Negative Immune Regulator that Inhibits Antitumor T-Cell Immunity. (PMID:31350312)
  • Downregulation of PIK3IP1 in retinal microglia promotes retinal pathological neovascularization via PI3K-AKT pathway activation. (PMID:37550343)
  • CircPDE5A-encoded novel regulator of the PI3K/AKT pathway inhibits esophageal squamous cell carcinoma progression by promoting USP14-mediated de-ubiquitination of PIK3IP1. (PMID:38658954)

Cross-species orthologs

14 orthologs

OrganismSymbolGene ID
danio_reriopik3ip1ENSDARG00000003281
mus_musculusPik3ip1ENSMUSG00000034614
rattus_norvegicusPik3ip1ENSRNOG00000018859
drosophila_melanogasterCG14780FBGN0025383
drosophila_melanogasterCG14227FBGN0031058
drosophila_melanogasterCG11664FBGN0040341
drosophila_melanogasterCG30287FBGN0050287
drosophila_melanogasterCG30288FBGN0050288
drosophila_melanogasterCG30289FBGN0050289
drosophila_melanogasterCG30414FBGN0050414
drosophila_melanogasterCG31205FBGN0051205
drosophila_melanogasterCG33225FBGN0053225
drosophila_melanogasterCG33226FBGN0069056
drosophila_melanogasterCG30283FBGN0260477

Paralogs (5): HGF (ENSG00000019991), GZMK (ENSG00000113088), GZMA (ENSG00000145649), HABP2 (ENSG00000148702), MST1 (ENSG00000173531)

Protein

Protein identifiers

Phosphoinositide-3-kinase-interacting protein 1Q96FE7 (reviewed: Q96FE7)

Alternative names: Kringle domain-containing protein HGFL

All UniProt accessions (2): C9JMK5, Q96FE7

UniProt curated annotations — full annotation on UniProt →

Function. Negative regulator of hepatic phosphatidylinositol 3-kinase (PI3K) activity.

Subcellular location. Cell membrane.

Post-translational modifications. N- and O-glycosylated. O-glycosylated with core 1 or possibly core 8 glycans. N-glycan heterogeneity at Asn-66: dHex1Hex5HexNAc4 (major) and dHex1Hex6HexNAc5 (minor).

Isoforms (5)

UniProt IDNamesCanonical?
Q96FE7-11, HGFL(L)yes
Q96FE7-22, HGFL(S)
Q96FE7-33
Q96FE7-44
Q96FE7-55, PIK3IP1-v1

RefSeq proteins (2): NP_001129383, NP_443112* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000001KringleDomain
IPR013806Kringle-likeHomologous_superfamily
IPR018056Kringle_CSConserved_site
IPR038178Kringle_sfHomologous_superfamily

Pfam: PF00051

UniProt features (21 total): splice variant 5, disulfide bond 3, sequence conflict 2, topological domain 2, glycosylation site 2, signal peptide 1, chain 1, sequence variant 1, transmembrane region 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96FE7-F167.900.14

Functional residue map

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

Disulfide bonds (3): 25–101, 46–82, 70–96

Glycosylation sites (2): 39, 66

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 335 (showing top): KOBAYASHI_EGFR_SIGNALING_24HR_UP, ATACCTC_MIR202, NFKB_Q6, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, HAHTOLA_MYCOSIS_FUNGOIDES_DN, GTGCCTT_MIR506, MODULE_379, GOBP_NEGATIVE_REGULATION_OF_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, ROZANOV_MMP14_TARGETS_UP, GOBP_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, GGARNTKYCCA_UNKNOWN, LEE_EARLY_T_LYMPHOCYTE_DN, HIF1_Q3, P300_01, MODULE_242

GO Biological Process (1): negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051898)

GO Molecular Function (4): endopeptidase activity (GO:0004175), signaling receptor binding (GO:0005102), phosphatidylinositol 3-kinase inhibitor activity (GO:0141039), protein binding (GO:0005515)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
phosphatidylinositol 3-kinase/protein kinase B signal transduction1
regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction1
negative regulation of intracellular signal transduction1
peptidase activity1
protein binding1
phosphatidylinositol 3-kinase regulator activity1
binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

570 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PIK3IP1PIK3CAP42336533
PIK3IP1LRRC14BA6NHZ5448
PIK3IP1LRRC14Q15048424
PIK3IP1DNAJC30Q96LL9421
PIK3IP1H7C2Y5H7C2Y5417
PIK3IP1BAHD1Q8TBE0400
PIK3IP1ARID1AO14497396
PIK3IP1PIP4K2CQ8TBX8394
PIK3IP1PIP4K2BP78356391
PIK3IP1PIP4K2AP48426375
PIK3IP1TAF3Q5VWG9371
PIK3IP1MXD4Q14582369
PIK3IP1SAMD10Q9BYL1366
PIK3IP1PLEKHF1Q96S99364
PIK3IP1PIK3R3Q92569358

IntAct

29 interactions, top by confidence:

ABTypeScore
UBQLN1PIK3IP1psi-mi:“MI:0915”(physical association)0.560
PIK3IP1UBQLN1psi-mi:“MI:0915”(physical association)0.560
PIK3IP1UBQLN2psi-mi:“MI:0915”(physical association)0.560
MAGEA11PIK3IP1psi-mi:“MI:0915”(physical association)0.560
SLC35A1PIK3IP1psi-mi:“MI:0915”(physical association)0.560
MFSD11PIK3IP1psi-mi:“MI:0915”(physical association)0.560
TMEM218PIK3IP1psi-mi:“MI:0915”(physical association)0.560
UPK1BPIK3IP1psi-mi:“MI:0915”(physical association)0.560
PIK3IP1TFRCpsi-mi:“MI:0914”(association)0.350
PIK3IP1PODXLpsi-mi:“MI:0914”(association)0.350
PIK3IP1POTEFpsi-mi:“MI:0914”(association)0.350
PIK3IP1SEL1L3psi-mi:“MI:0914”(association)0.350
PIK3IP1UBQLN2psi-mi:“MI:0915”(physical association)0.000
PIK3IP1MAGEA11psi-mi:“MI:0915”(physical association)0.000
SLC35A1PIK3IP1psi-mi:“MI:0915”(physical association)0.000
MFSD11PIK3IP1psi-mi:“MI:0915”(physical association)0.000
UPK1BPIK3IP1psi-mi:“MI:0915”(physical association)0.000
TMEM218PIK3IP1psi-mi:“MI:0915”(physical association)0.000

BioGRID (20): PIK3IP1 (Two-hybrid), PIK3IP1 (Two-hybrid), UPK1B (Two-hybrid), TMEM218 (Two-hybrid), SLC35A1 (Two-hybrid), MAGEA11 (Two-hybrid), UBQLN2 (Two-hybrid), EPHA7 (Affinity Capture-MS), FAM114A2 (Affinity Capture-MS), IPO7 (Affinity Capture-MS), SAAL1 (Affinity Capture-MS), TFRC (Affinity Capture-MS), GOLGB1 (Affinity Capture-MS), SRPR (Affinity Capture-MS), PODXL (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GSZ0, A0A1B0GUA5, A0A1B0GVQ0, A0A1B0GVT2, A0JNM1, A2A9G7, A2APA5, A2VE22, A6NLX4, A7E1Z1, A7MB05, A9CBA0, D3ZR35, E9Q942, F5HI25, O39519, P06480, P09517, P0DJ93, P18345, Q0II74, Q0VFL4, Q1RMT9, Q2T9Z2, Q498C7, Q56A20, Q5BIR3, Q5RCS3, Q5XIF1, Q67593, Q6UWT2, Q6UWV7, Q7TMJ8, Q80WB0, Q80WK2, Q86UW2, Q8K1D8, Q8N5W8, Q8TEF2, Q8VEA7

Diamond homologs: D3ZTE0, O18783, O97507, P00734, P00747, P00750, P04185, P06867, P06868, P06869, P08519, P11214, P12545, P14210, P15638, P19221, P19637, P20918, P26927, P26928, P29598, P49150, P80009, P98119, P98121, Q01177, Q04756, Q04962, Q05589, Q14520, Q1RMT9, Q24K22, Q28198, Q29485, Q56A20, Q5E9Z2, Q5R537, Q5R8J0, Q5R8X6, Q5RCS3

SIGNOR signaling

2 interactions.

AEffectBMechanism
CUX1“down-regulates quantity by repression”PIK3IP1“transcriptional regulation”
PIK3IP1“down-regulates activity”PI3Kbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance36
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

935 predictions. Top by Δscore:

VariantEffectΔscore
22:31289311:TGA:Tdonor_loss1.0000
22:31289312:GAC:Gdonor_loss1.0000
22:31289313:A:ACdonor_gain1.0000
22:31289314:C:CCdonor_gain1.0000
22:31289314:CCT:Cdonor_gain1.0000
22:31289390:TAGC:Tacceptor_gain1.0000
22:31289391:AGC:Aacceptor_gain1.0000
22:31289392:GC:Gacceptor_gain1.0000
22:31289392:GCC:Gacceptor_loss1.0000
22:31289393:CC:Cacceptor_gain1.0000
22:31289393:CCTG:Cacceptor_loss1.0000
22:31289394:C:Aacceptor_loss1.0000
22:31289394:C:CCacceptor_gain1.0000
22:31289395:T:Cacceptor_loss1.0000
22:31289398:C:CTacceptor_gain1.0000
22:31289398:C:Tacceptor_gain1.0000
22:31289399:A:Tacceptor_gain1.0000
22:31289403:A:ACacceptor_gain1.0000
22:31289403:A:Cacceptor_gain1.0000
22:31289493:TCATA:Tdonor_loss1.0000
22:31289495:ATACC:Adonor_loss1.0000
22:31289496:TACC:Tdonor_loss1.0000
22:31289497:A:ACdonor_gain1.0000
22:31289497:AC:Adonor_gain1.0000
22:31289498:C:CCdonor_gain1.0000
22:31289498:CC:Cdonor_gain1.0000
22:31289510:AGGT:Adonor_gain1.0000
22:31289513:T:TAdonor_gain1.0000
22:31289700:C:CCacceptor_gain1.0000
22:31291081:GCCC:Gacceptor_gain1.0000

AlphaMissense

1703 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:31291220:C:AW49C0.995
22:31291220:C:GW49C0.995
22:31291029:C:AW81C0.993
22:31291029:C:GW81C0.993
22:31291027:C:GC82S0.990
22:31291028:A:TC82S0.990
22:31291063:C:GC70S0.988
22:31291064:A:TC70S0.988
22:31291060:C:GR71P0.987
22:31291230:C:GC46S0.986
22:31291231:A:TC46S0.986
22:31283207:G:CF223L0.985
22:31283207:G:TF223L0.985
22:31283209:A:GF223L0.985
22:31291026:G:CC82W0.984
22:31289342:C:TG187D0.983
22:31289348:C:TG185E0.983
22:31289343:C:GG187R0.980
22:31289349:C:GG185R0.980
22:31289349:C:TG185R0.980
22:31291028:A:GC82R0.980
22:31289330:C:TG191D0.978
22:31291063:C:TC70Y0.977
22:31289317:C:AK195N0.975
22:31289317:C:GK195N0.975
22:31289381:C:TG174D0.974
22:31291062:G:CC70W0.974
22:31291064:A:GC70R0.974
22:31291231:A:GC46R0.974
22:31289372:A:TM177K0.973

dbSNP variants (sampled 300 via entrez): RS1000017898 (22:31287127 C>T), RS1000402658 (22:31282510 C>G,T), RS1000514021 (22:31287630 A>G,T), RS1000623513 (22:31288779 A>G), RS1000684296 (22:31294128 A>C), RS1000718264 (22:31293437 A>C), RS1000914825 (22:31289054 CTT>C), RS1000948194 (22:31287162 C>T), RS1001194897 (22:31293661 CTT>C,CT,CTTT,CTTTT), RS1001253724 (22:31293187 C>T), RS1001992251 (22:31286317 G>A), RS1002262666 (22:31294287 C>G), RS1002425206 (22:31289495 A>G), RS1002654907 (22:31283643 C>G), RS1002954441 (22:31283994 T>C)

Disease associations

OMIM: gene MIM:619158 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST009391_620Metabolite levels7.000000e-06
GCST010135_20Oily fish consumption3.000000e-10
GCST010135_5Oily fish consumption1.000000e-15
GCST010140_12Pork consumption3.000000e-10
GCST010140_49Pork consumption1.000000e-15
GCST010142_11Fish- and plant-related diet1.000000e-11
GCST010142_79Fish- and plant-related diet3.000000e-08
GCST90002404_593Red cell distribution width7.000000e-16

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0009793isoleucine measurement
EFO:0008111diet measurement
EFO:0009188Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionaffects expression, decreases expression, decreases methylation3
Acetaminophendecreases expression, increases expression2
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation2
Estradiolaffects cotreatment, increases expression, decreases expression2
Tretinoinincreases expression2
Valproic Acidaffects expression, decreases expression2
Cyclosporinedecreases expression2
aristolochic acid Iincreases expression1
GSK-J4increases expression1
sotorasibaffects cotreatment, increases expression1
pirinixic aciddecreases expression, increases activity, affects binding1
bisphenol Aincreases expression1
nickel chlorideincreases expression1
potassium chromate(VI)decreases expression1
aflatoxin B2increases methylation1
hydroquinonedecreases expression1
avobenzoneincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluoro-n-nonanoic aciddecreases expression1
motexafin gadoliniumincreases expression, affects cotreatment1
nutlin 3affects cotreatment, increases expression1
abrineincreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidineincreases expression1
bisphenol Sdecreases expression1
idelalisibincreases expression1
trametinibaffects cotreatment, increases expression1
1-(4-((2-(2-aminopyrimidin-5-yl)-7-methyl-4-morpholinothieno(3,2-d)pyrimidin-6-yl)methyl)piperazin-1-yl)-2-hydroxypropan-1-oneincreases expression1
NVP-BKM120affects cotreatment, increases expression1
Sunitinibdecreases expression1
Air Pollutantsincreases abundance, decreases 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.