PITPNC1

gene
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Also known as RDGBB1RDGBBRDGB-BETA

Summary

PITPNC1 (phosphatidylinositol transfer protein cytoplasmic 1, HGNC:21045) is a protein-coding gene on chromosome 17q24.2, encoding Cytoplasmic phosphatidylinositol transfer protein 1 (Q9UKF7). Catalyzes the transfer of phosphatidylinositol (PI) and phosphatidic acid (PA) between membranes.

This gene encodes a member of the phosphatidylinositol transfer protein family. The encoded cytoplasmic protein plays a role in multiple processes including cell signaling and lipid metabolism by facilitating the transfer of phosphatidylinositol between membrane compartments. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 1.

Source: NCBI Gene 26207 — RefSeq curated summary.

At a glance

  • GWAS associations: 15
  • Clinical variants (ClinVar): 20 total
  • MANE Select transcript: NM_012417

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21045
Approved symbolPITPNC1
Namephosphatidylinositol transfer protein cytoplasmic 1
Location17q24.2
Locus typegene with protein product
StatusApproved
AliasesRDGBB1, RDGBB, RDGB-BETA
Ensembl geneENSG00000154217
Ensembl biotypeprotein_coding
OMIM605134
Entrez26207

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 retained_intron

ENST00000578527, ENST00000580974, ENST00000581322, ENST00000581923, ENST00000584471, ENST00000584554

RefSeq mRNA: 2 — MANE Select: NM_012417 NM_012417, NM_181671

CCDS: CCDS58587, CCDS58588

Canonical transcript exons

ENST00000581322 — 9 exons

ExonStartEnd
ENSE000026944506737728167378202
ENSE000027212716769257267697256
ENSE000027238006755361067553617
ENSE000035026826755225767552345
ENSE000035150446766950867669663
ENSE000035723536767547967675542
ENSE000035890116763214367632238
ENSE000036326516757818667578257
ENSE000036803596753280267532950

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 96.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.5173 / max 231.7990, expressed in 1756 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
16233217.53671722
1623332.95441218
1623342.1530792
1623310.4155246
2083550.3354170
1623360.122362

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011596.76gold quality
cortical plateUBERON:000534395.97gold quality
cartilage tissueUBERON:000241895.34gold quality
Brodmann (1909) area 23UBERON:001355495.07gold quality
lateral nuclear group of thalamusUBERON:000273694.46gold quality
dorsal motor nucleus of vagus nerveUBERON:000287093.77gold quality
middle temporal gyrusUBERON:000277193.62gold quality
parotid glandUBERON:000183193.15gold quality
palpebral conjunctivaUBERON:000181292.96gold quality
islet of LangerhansUBERON:000000692.13gold quality
granulocyteCL:000009492.11gold quality
bloodUBERON:000017891.68gold quality
germinal epithelium of ovaryUBERON:000130491.63gold quality
caudate nucleusUBERON:000187390.99gold quality
medial globus pallidusUBERON:000247790.98gold quality
nucleus accumbensUBERON:000188290.87gold quality
entorhinal cortexUBERON:000272890.82gold quality
eyeUBERON:000097090.78gold quality
pericardiumUBERON:000240790.76gold quality
superior frontal gyrusUBERON:000266190.46gold quality
postcentral gyrusUBERON:000258190.42gold quality
cranial nerve IIUBERON:000094190.36gold quality
primary visual cortexUBERON:000243690.36gold quality
pancreasUBERON:000126490.22gold quality
putamenUBERON:000187489.95gold quality
omental fat padUBERON:001041489.70gold quality
peritoneumUBERON:000235889.67gold quality
globus pallidusUBERON:000187589.62gold quality
leukocyteCL:000073889.60gold quality
body of pancreasUBERON:000115089.60gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-35yes3404.12
E-GEOD-180759yes2720.30
E-HCAD-25yes2521.95
E-CURD-119yes26.35
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

167 targeting PITPNC1, 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-190A-3P100.0080.355520
HSA-MIR-3163100.0077.238605
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-3646100.0073.565283
HSA-MIR-188-3P100.0068.761240
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4481100.0066.421669
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-428299.9975.366408
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-453199.9969.703181
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-548P99.9872.253784
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-548N99.9871.944170
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-548AN99.9770.912817
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-60799.9773.625593
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753

Literature-anchored findings (GeneRIF, showing 9)

  • The phosphatidylinositol transfer protein RdgBbeta binds 14-3-3 via its unstructured C-terminus, whereas its lipid-binding domain interacts with the integral membrane protein ATRAP (angiotensin II type I receptor-associated protein). (PMID:21728994)
  • Phosphatidylinositol transfer protein, cytoplasmic 1 (PITPNC1) binds and transfers phosphatidic acid (PMID:22822086)
  • The most significantly associated SNPs to type 2 diabetes mellitus in this study are expression SNPs to the lymphocyte antigen 75 gene, the ubiquitin-specific peptidase 36 gene, and the phosphatidylinositol transfer protein, cytoplasmic 1 gene. (PMID:22865700)
  • PITPNC1-mediated vesicular release. (PMID:26977884)
  • We propose that Pitpnc1a-expressing neurons alter behavior via modification of neuro-modulatory IGF that acts on downstream wake-promoting circuits (PMID:30089250)
  • Elevated expression of PITPNC1 in gastric cancer is correlated with an advanced clinical stage and a poor prognosis. PITPNC1 promotes anoikis resistance through enhanced fatty acid oxidation, which is regulated by omental adipocytes and consequently facilitates gastric cancer omental metastasis. (PMID:30555557)
  • Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription. (PMID:35292404)
  • The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer. (PMID:37210549)
  • PITPNC1 Suppress CD8[+] T cell immune function and promote radioresistance in rectal cancer by modulating FASN/CD155. (PMID:38291470)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
danio_rerioPITPNC1ENSDARG00000099260
rattus_norvegicusPitpnc1ENSRNOG00000069160

Paralogs (5): PITPNM2 (ENSG00000090975), PITPNM3 (ENSG00000091622), PITPNM1 (ENSG00000110697), PITPNA (ENSG00000174238), PITPNB (ENSG00000180957)

Protein

Protein identifiers

Cytoplasmic phosphatidylinositol transfer protein 1Q9UKF7 (reviewed: Q9UKF7)

Alternative names: Mammalian rdgB homolog beta, Retinal degeneration B homolog beta

All UniProt accessions (4): Q9UKF7, A0A0C4DGP0, J3QRS7, J3QS95

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the transfer of phosphatidylinositol (PI) and phosphatidic acid (PA) between membranes. Binds PA derived from the phospholipase D signaling pathway and among the cellular PA species, preferably binds to the C16:0/16:1 and C16:1/18:1 PA species. Catalyzes the transfer of phosphatidylinositol between membranes.

Subcellular location. Cytoplasm.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the PtdIns transfer protein family. PI transfer class IIB subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q9UKF7-11, sp1yes
Q9UKF7-22, sp2

RefSeq proteins (2): NP_036549, NP_858057 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001666PI_transferFamily
IPR023393START-like_dom_sfHomologous_superfamily
IPR055261PI_transfer_NDomain

Pfam: PF02121

Catalyzed reactions (Rhea), 2 shown:

  • a 1,2-diacyl-sn-glycero-3-phosphate(in) = a 1,2-diacyl-sn-glycero-3-phosphate(out) (RHEA:36435)
  • a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol)(in) = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol)(out) (RHEA:38691)

UniProt features (13 total): sequence conflict 4, modified residue 4, compositionally biased region 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UKF7-F183.270.67

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): 119, 270, 274, 278

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 337 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, AHRARNT_01, AGGAAGC_MIR5163P, GCM_MAP4K4, FREAC2_01, MODULE_255, AAGCCAT_MIR135A_MIR135B, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, MODULE_317, RACCACAR_AML_Q6, FOXO4_01, AP2_Q3, GGGTGGRR_PAX4_03, COUP_01

GO Biological Process (4): signal transduction (GO:0007165), phospholipid transport (GO:0015914), lipid transport (GO:0006869), intermembrane lipid transfer (GO:0120009)

GO Molecular Function (8): phosphatidylinositol transfer activity (GO:0008526), phosphatidylinositol binding (GO:0035091), phosphatidic acid binding (GO:0070300), phosphatidylglycerol binding (GO:1901611), phosphatidic acid transfer activity (GO:1990050), protein binding (GO:0005515), obsolete phospholipid transporter activity (GO:0005548), lipid binding (GO:0008289)

GO Cellular Component (4): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
anion binding3
cellular anatomical structure3
lipid transport2
phospholipid binding2
binding2
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
organophosphate ester transport1
transport1
lipid localization1
membrane organization1
phosphatidylinositol binding1
lipid transfer activity1
phospholipid transfer activity1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PITPNC1RAB1BQ9H0U4880
PITPNC1AGTRAPQ6RW13602
PITPNC1HELZP42694537
PITPNC1MERTKQ12866472
PITPNC1IGFBP2P18065469
PITPNC1MYO18AQ92614438
PITPNC1PRKACAP17612430
PITPNC1PRKACBP22694430
PITPNC1PRKACGP22612429
PITPNC1RADILQ96JH8395
PITPNC1PTPREP23469389
PITPNC1MYO5BQ9ULV0374
PITPNC1GOLPH3Q9H4A6369
PITPNC1PITPNAQ00169361
PITPNC1ARFGEF3Q5TH69354

IntAct

15 interactions, top by confidence:

ABTypeScore
AGTRAPPITPNC1psi-mi:“MI:0915”(physical association)0.760
PITPNC1AGTRAPpsi-mi:“MI:0915”(physical association)0.760
PITPNC1CMTM5psi-mi:“MI:0915”(physical association)0.560
CMTM5PITPNC1psi-mi:“MI:0915”(physical association)0.560
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
YWHABSHTN1psi-mi:“MI:0914”(association)0.530
YWHAZSHTN1psi-mi:“MI:0914”(association)0.530
Psmd6MIF4GDpsi-mi:“MI:0914”(association)0.350
YWHAHSHTN1psi-mi:“MI:0914”(association)0.350

BioGRID (27): AGTRAP (Two-hybrid), CMTM5 (Two-hybrid), AGTRAP (Two-hybrid), PITPNC1 (Affinity Capture-MS), PITPNC1 (Two-hybrid), PITPNC1 (Two-hybrid), PITPNC1 (Two-hybrid), PITPNC1 (Two-hybrid), PITPNC1 (Two-hybrid), PITPNC1 (Two-hybrid), PITPNC1 (Two-hybrid), CACFD1 (Two-hybrid), ANKS6 (Two-hybrid), CMTM5 (Two-hybrid), TNFRSF10D (Two-hybrid)

ESM2 similar proteins: A0A076FF10, A0A076FFM5, B3P9N0, B4PY69, B4R313, B6JWP7, D6WMX4, F7J184, F7J186, F7J187, F7J188, H9N289, H9N290, O13861, O14249, O14349, O42411, O42449, O46084, O74787, O81000, O81395, P34426, P49896, P51820, P53264, P95483, Q05763, Q06510, Q17938, Q1JUZ1, Q1JUZ2, Q21407, Q28CA0, Q2QEI3, Q2QRX6, Q38932, Q68EW0, Q6DHJ3, Q755Y0

Diamond homologs: G5EEM9, O00562, O35954, O46606, P16446, P43125, P48738, P48739, P53810, P53811, P53812, Q00169, Q28CA0, Q2HJ54, Q3UHE1, Q54D93, Q54VC7, Q5R6F0, Q5U2N3, Q6NZC7, Q6ZPQ6, Q80YA3, Q8K4R4, Q8NEL9, Q8W5R2, Q9BZ71, Q9BZ72, Q9NCL7, Q9NCL8, Q9TR36, Q9U9P7, Q9UKF7, Q12204

SIGNOR signaling

2 interactions.

AEffectBMechanism
PRKCA“up-regulates activity”PITPNC1phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance13
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4271 predictions. Top by Δscore:

VariantEffectΔscore
17:67378199:CGAGG:Cdonor_loss1.0000
17:67378201:AGGT:Adonor_loss1.0000
17:67378203:G:Cdonor_loss1.0000
17:67378204:T:Gdonor_loss1.0000
17:67431812:A:Gdonor_gain1.0000
17:67438855:GCCA:Gdonor_gain1.0000
17:67532800:A:AGacceptor_gain1.0000
17:67532800:A:ATacceptor_loss1.0000
17:67532801:G:GCacceptor_gain1.0000
17:67532801:GT:Gacceptor_gain1.0000
17:67532801:GTA:Gacceptor_gain1.0000
17:67532801:GTAC:Gacceptor_gain1.0000
17:67532801:GTACA:Gacceptor_gain1.0000
17:67532948:CAGGT:Cdonor_loss1.0000
17:67532949:AGGT:Adonor_loss1.0000
17:67532950:GGT:Gdonor_loss1.0000
17:67532952:T:Adonor_loss1.0000
17:67553590:A:AGacceptor_gain1.0000
17:67553618:G:GGdonor_gain1.0000
17:67578183:CAG:Cacceptor_loss1.0000
17:67578184:A:AGacceptor_gain1.0000
17:67578184:AGT:Aacceptor_gain1.0000
17:67578185:G:GTacceptor_gain1.0000
17:67578185:GT:Gacceptor_gain1.0000
17:67578185:GTG:Gacceptor_gain1.0000
17:67578185:GTGT:Gacceptor_gain1.0000
17:67578185:GTGTT:Gacceptor_gain1.0000
17:67578258:G:GGdonor_gain1.0000
17:67632132:T:Aacceptor_gain1.0000
17:67632138:TTCA:Tacceptor_loss1.0000

AlphaMissense

2193 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:67378174:G:CR7P1.000
17:67378186:C:AP11Q1.000
17:67378189:T:CL12P1.000
17:67532802:T:CY17H1.000
17:67532811:G:AG20R1.000
17:67532811:G:CG20R1.000
17:67532812:G:AG20E1.000
17:67532812:G:TG20V1.000
17:67532818:T:CL22P1.000
17:67532820:T:GY23D1.000
17:67532836:A:CH28P1.000
17:67532865:G:AG38R1.000
17:67532865:G:CG38R1.000
17:67532865:G:TG38W1.000
17:67532866:G:AG38E1.000
17:67532916:G:TG55W1.000
17:67532917:G:AG55E1.000
17:67532933:G:CK60N1.000
17:67532933:G:TK60N1.000
17:67532935:G:CR61P1.000
17:67552270:T:AW71R1.000
17:67552270:T:CW71R1.000
17:67552271:G:CW71S1.000
17:67552272:G:CW71C1.000
17:67552272:G:TW71C1.000
17:67552274:C:AA72D1.000
17:67552283:T:AV75D1.000
17:67552310:A:TE84V1.000
17:67552311:G:CE84D1.000
17:67552311:G:TE84D1.000

dbSNP variants (sampled 300 via entrez): RS1000007752 (17:67554118 G>A), RS1000020659 (17:67431146 C>G), RS1000029805 (17:67438218 T>C,G), RS1000057782 (17:67609579 C>T), RS1000062940 (17:67472281 G>A), RS1000067479 (17:67393619 A>C,T), RS1000070955 (17:67397749 T>C), RS1000085835 (17:67517574 T>C), RS1000086922 (17:67643198 G>A), RS1000094551 (17:67377402 G>A), RS1000120592 (17:67541261 G>A), RS1000128674 (17:67687833 C>A,T), RS1000133451 (17:67602947 C>T), RS1000167112 (17:67668233 T>C), RS1000172768 (17:67567997 G>T)

Disease associations

OMIM: gene MIM:605134 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

15 associations (top):

StudyTraitp-value
GCST002113_5Pulmonary function3.000000e-06
GCST002349_4Response to protease inhibitor treatment in hepatitis c (peak serum total bilirubin levels)3.000000e-06
GCST002875_91Diisocyanate-induced asthma6.000000e-07
GCST005986_28Blood urea nitrogen levels9.000000e-13
GCST006416_3Chronic central serous retinopathy2.000000e-07
GCST007565_179Morning person3.000000e-14
GCST007576_246Chronotype3.000000e-14
GCST008058_2Estimated glomerular filtration rate4.000000e-10
GCST008062_52Blood urea nitrogen levels9.000000e-22
GCST010118_64Type 2 diabetes2.000000e-08
GCST010146_43Serum immune biomarker levels1.000000e-08
GCST010989_273Body size at age 102.000000e-08
GCST012070_3Plasma selenium concentration3.000000e-07
GCST90020025_1487Waist-to-hip ratio adjusted for BMI6.000000e-09
GCST90020027_512Waist-hip index4.000000e-09

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0003892pulmonary function measurement
EFO:0004713FEV/FVC ratio
EFO:0004570bilirubin measurement
EFO:0005657response to protease inhibitor
EFO:0006995response to diisocyanate
EFO:0009363chronic central serous retinopathy
EFO:0008328chronotype measurement
EFO:0004869YKL40 measurement
EFO:0004872inflammatory biomarker measurement
EFO:0009819comparative body size at age 10, self-reported
EFO:0007788BMI-adjusted waist-hip ratio

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
Benzo(a)pyreneaffects methylation, decreases expression6
trichostatin Aaffects cotreatment, decreases expression3
Valproic Acidaffects expression, decreases expression, decreases methylation3
Aflatoxin B1increases methylation, affects expression, decreases methylation3
Temozolomideaffects response to substance, decreases expression2
Acetaminophenincreases expression2
Doxorubicindecreases expression, affects response to substance2
Estradiolaffects cotreatment, decreases expression, increases expression2
Formaldehydeincreases expression, decreases expression2
Tobacco Smoke Pollutiondecreases methylation, increases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
methylmercuric chlorideincreases expression1
sodium arsenitedecreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)decreases expression1
cupric chloridedecreases expression1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphindecreases expression, affects cotreatment1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Sunitinibincreases expression1
Arsenic Trioxideincreases expression1
Vorinostatdecreases expression1
Arsenicaffects methylation1
Azacitidinedecreases expression1
Cadmiumdecreases expression1
Caffeinedecreases phosphorylation1
Carmustineaffects response to substance1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hepatitis C virus infection