PDCL

gene
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Also known as PhLPDKFZp564M1863

Summary

PDCL (phosducin like, HGNC:8770) is a protein-coding gene on chromosome 9q33.2, encoding Phosducin-like protein (Q13371). Acts as a positive regulator of hedgehog signaling and regulates ciliary function. It is a selective cancer dependency (DepMap: 30.0% of cell lines).

Phosducin-like protein is a putative modulator of heterotrimeric G proteins. The protein shares extensive amino acid sequence homology with phosducin, a phosphoprotein expressed in retina and pineal gland. Both phosducin-like protein and phosphoducin have been shown to regulate G-protein signaling by binding to the beta-gamma subunits of G proteins.

Source: NCBI Gene 5082 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 46 total
  • Cancer dependency (DepMap): dependent in 30.0% of screened cell lines
  • MANE Select transcript: NM_005388

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8770
Approved symbolPDCL
Namephosducin like
Location9q33.2
Locus typegene with protein product
StatusApproved
AliasesPhLP, DKFZp564M1863
Ensembl geneENSG00000136940
Ensembl biotypeprotein_coding
OMIM604421
Entrez5082

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000259467, ENST00000394285, ENST00000436632, ENST00000935271, ENST00000935272, ENST00000935273, ENST00000943131

RefSeq mRNA: 1 — MANE Select: NM_005388 NM_005388

CCDS: CCDS6845

Canonical transcript exons

ENST00000259467 — 4 exons

ExonStartEnd
ENSE00000806541122826616122826792
ENSE00000927037122823016122823197
ENSE00001091240122818097122820636
ENSE00001517952122828471122828588

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 97.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.3028 / max 214.7140, expressed in 1817 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
10239522.37081814
1023940.9321648

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233697.64gold quality
endothelial cellCL:000011596.70silver quality
visceral pleuraUBERON:000240194.18gold quality
oocyteCL:000002393.45gold quality
parietal pleuraUBERON:000240092.86gold quality
tibiaUBERON:000097992.73gold quality
pleuraUBERON:000097792.46gold quality
calcaneal tendonUBERON:000370192.32gold quality
secondary oocyteCL:000065591.89gold quality
cervix squamous epitheliumUBERON:000692291.63silver quality
germinal epithelium of ovaryUBERON:000130491.04gold quality
epithelium of nasopharynxUBERON:000195190.05gold quality
nasopharynxUBERON:000172890.04gold quality
tendonUBERON:000004389.58gold quality
oral cavityUBERON:000016789.42gold quality
ganglionic eminenceUBERON:000402389.09gold quality
trabecular bone tissueUBERON:000248388.33gold quality
stromal cell of endometriumCL:000225588.15gold quality
embryoUBERON:000092288.06gold quality
periodontal ligamentUBERON:000826688.02gold quality
pigmented layer of retinaUBERON:000178287.86gold quality
retinaUBERON:000096687.83gold quality
superficial temporal arteryUBERON:000161487.71gold quality
seminal vesicleUBERON:000099887.66gold quality
cauda epididymisUBERON:000436087.66gold quality
adult organismUBERON:000702387.58gold quality
cortical plateUBERON:000534387.49gold quality
gingival epitheliumUBERON:000194987.48silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.43gold quality
choroid plexus epitheliumUBERON:000391187.09gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

80 targeting PDCL, 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-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-1213699.9872.815713
HSA-MIR-477599.9875.006394
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-426799.9666.532368
HSA-MIR-590-3P99.9674.346478
HSA-MIR-570-3P99.9672.414910
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-211099.9666.681930
HSA-MIR-651-3P99.9473.485177
HSA-MIR-539-5P99.9370.302855
HSA-MIR-311999.9271.342390
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-153-5P99.8973.866317
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-94499.8270.853042
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-451799.7669.191867
HSA-MIR-92A-2-5P99.7567.012164

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 30.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 7)

  • physiological control of G-protein regulation by PhLP seems to involve phosphorylation by CK2 and alternative splicing of the regulator (PMID:12466282)
  • the strong inhibitory action of PhLP(S) on Gbetagamma signaling is the result of a previously unrecognized mechanism of Gbetagamma-regulation, inhibition of Gbetagamma-folding by interference with TCP-1alpha (PMID:15745879)
  • PhLP phosphorylation permits the release of a PhLP x Gbeta intermediate from cytosolic chaperonin complex, allowing Ggamma to associate with Gbeta in this intermediate complex. (PMID:16717095)
  • cytosolic chaperonin complex-dependent mechanism exists for Gbeta5-RGS7 assembly that utilizes the co-chaperone activity of PhLP1 in a unique way (PMID:19376773)
  • PhLP-M1-G149, a Gbetagamma-interacting construct derived from phosducin-like protein 1 (PhLP) is a differential inhibitor of Gbetagamma (PMID:19403526)
  • evidence of a generic mechanism, whereby the splicing of the PhLP gene could potentially and efficiently regulate the cellular levels of heterotrimeric G proteins. (PMID:23888055)
  • PhLP1 binding stabilizes the Gbeta fold, disrupting interactions with CCT and releasing a PhLP1-Gbeta dimer for assembly with Ggamma. (PMID:25675501)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriopdclENSDARG00000009480
mus_musculusPdclENSMUSG00000009030
rattus_norvegicusPdclENSRNOG00000008484
rattus_norvegicusAABR07051787.1ENSRNOG00000059243
drosophila_melanogasterCG7650FBGN0036519
caenorhabditis_elegansWBGENE00003142

Paralogs (4): TXNDC9 (ENSG00000115514), PDCL3 (ENSG00000115539), PDC (ENSG00000116703), PDCL2 (ENSG00000163440)

Protein

Protein identifiers

Phosducin-like proteinQ13371 (reviewed: Q13371)

All UniProt accessions (3): Q13371, H0Y3M0, H0Y5D3

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a positive regulator of hedgehog signaling and regulates ciliary function. Functions as a co-chaperone for CCT in the assembly of heterotrimeric G protein complexes, facilitates the assembly of both Gbeta-Ggamma and RGS-Gbeta5 heterodimers. Acts as a negative regulator of heterotrimeric G proteins assembly by trapping the preloaded G beta subunits inside the CCT chaperonin.

Subunit / interactions. Forms a complex with the beta and gamma subunits of the GTP-binding protein, transducin. Interacts with the CCT chaperonin complex.

Subcellular location. Cell projection. Cilium.

Miscellaneous. Expressed ubiquitously, highest levels are found in neural tissues amounting to 10% of total PDCL mRNA.

Similarity. Belongs to the phosducin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q13371-11yes
Q13371-22, PhLPs

RefSeq proteins (1): NP_005379* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001200PhosducinFamily
IPR023196Phosducin_N_dom_sfHomologous_superfamily
IPR024253Phosducin_thioredoxin-like_domDomain
IPR036249Thioredoxin-like_sfHomologous_superfamily
IPR051499Phosducin-like_regFamily

Pfam: PF02114

UniProt features (34 total): helix 9, strand 8, modified residue 6, sequence conflict 2, turn 2, initiator methionine 1, chain 1, splice variant 1, sequence variant 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

19 structures.

PDBMethodResolution (Å)
8SH9ELECTRON MICROSCOPY2.7
8SHGELECTRON MICROSCOPY2.8
8SGCELECTRON MICROSCOPY2.9
8SHQELECTRON MICROSCOPY2.9
9NOQELECTRON MICROSCOPY2.9
9NRHELECTRON MICROSCOPY2.9
8SG8ELECTRON MICROSCOPY3
8SHAELECTRON MICROSCOPY3
8SHFELECTRON MICROSCOPY3
8SHLELECTRON MICROSCOPY3
8SHOELECTRON MICROSCOPY3
8SHPELECTRON MICROSCOPY3
8SHTELECTRON MICROSCOPY3
9NPWELECTRON MICROSCOPY3
9NOPELECTRON MICROSCOPY3.1
9NQ6ELECTRON MICROSCOPY3.1
9NRFELECTRON MICROSCOPY3.1
9NOCELECTRON MICROSCOPY3.17
8SFFELECTRON MICROSCOPY3.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13371-F176.660.40

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 (6): 296, 2, 20, 25, 226, 293

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6814122Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding

MSigDB gene sets: 132 (showing top): WHITEHURST_PACLITAXEL_SENSITIVITY, TTTGTAG_MIR520D, GCM_ZNF198, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, SHEPARD_BMYB_MORPHOLINO_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_REGULATION_OF_SMOOTHENED_SIGNALING_PATHWAY, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, MORF_EPHA7, BENPORATH_NOS_TARGETS, GOBP_SENSORY_PERCEPTION, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOBP_SMOOTHENED_SIGNALING_PATHWAY, GOBP_CELL_PROJECTION_ORGANIZATION

GO Biological Process (6): signal transduction (GO:0007165), visual perception (GO:0007601), regulation of G protein-coupled receptor signaling pathway (GO:0008277), cell projection organization (GO:0030030), positive regulation of smoothened signaling pathway (GO:0045880), heterotrimeric G-protein complex assembly (GO:1902605)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): cytoplasm (GO:0005737), cytosol (GO:0005829), cilium (GO:0005929), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Chaperonin-mediated protein folding1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
sensory perception of light stimulus1
G protein-coupled receptor signaling pathway1
regulation of signal transduction1
cellular component organization1
smoothened signaling pathway1
regulation of smoothened signaling pathway1
positive regulation of signal transduction1
protein-containing complex assembly1
binding1
intracellular anatomical structure1
cytoplasm1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

1090 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PDCLGHITMQ9H3K2771
PDCLSUCLG2Q96I99735
PDCLPFN3P60673716
PDCLPFN4Q8NHR9716
PDCLPEDS1A5PLL7714
PDCLGNGT1P63211688
PDCLPFN1P07737669
PDCLGNB1P04697662
PDCLSLC26A5P58743580
PDCLCOPS7AQ9UBW8580
PDCLFCER2P06734542
PDCLDNAJC14Q6Y2X3522
PDCLSCP2P22307480
PDCLTMEM45AQ9NWC5480
PDCLENPP3O14638479

IntAct

158 interactions, top by confidence:

ABTypeScore
PSMC5PDCLpsi-mi:“MI:0915”(physical association)0.920
PDCLPSMC5psi-mi:“MI:0915”(physical association)0.920
CCT3PDCLpsi-mi:“MI:0915”(physical association)0.800
PSMC5PSMD11psi-mi:“MI:0914”(association)0.730
CCT2TXNDC9psi-mi:“MI:0914”(association)0.730
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
CCT2PPP6Cpsi-mi:“MI:0914”(association)0.640
PDCL3PEX7psi-mi:“MI:0914”(association)0.640
GNB1GNG7psi-mi:“MI:0914”(association)0.640
CCT3TXNDC9psi-mi:“MI:0914”(association)0.640
CCT5TXNDC9psi-mi:“MI:0914”(association)0.640
CCT7TXNDC9psi-mi:“MI:0914”(association)0.640
DCAF12L2CETN3psi-mi:“MI:0914”(association)0.640
GNG8GNB5psi-mi:“MI:0914”(association)0.640
GNG5GNB5psi-mi:“MI:0914”(association)0.620
PDCLMRPL11psi-mi:“MI:0915”(physical association)0.560
PDCLATN1psi-mi:“MI:0915”(physical association)0.560
KLK6PDCLpsi-mi:“MI:0915”(physical association)0.560

BioGRID (214): PSMC5 (Two-hybrid), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PDCL (Affinity Capture-MS), PSMC5 (Two-hybrid), PDCL (Proximity Label-MS), PDCL (Proximity Label-MS), PDCL (Proximity Label-MS)

ESM2 similar proteins: A0JM23, A5PMF7, B8JKF4, F4JZJ2, O23052, O60502, O77560, P0CF65, P0CI65, P19632, P20941, P20942, P41686, Q008S8, Q0P564, Q13371, Q2HJA9, Q2TBM9, Q3U213, Q568B8, Q58CZ2, Q5FVM7, Q5R7K4, Q5RCM7, Q5SNQ7, Q5ZKZ4, Q63737, Q68EV9, Q692V3, Q6AZT7, Q6P3V7, Q6P5D8, Q75BD8, Q80TN4, Q8BHD8, Q8S8L9, Q8VC33, Q8VIJ5, Q8VZQ0, Q94HV8

Diamond homologs: O77560, P19632, P20941, P20942, P41686, Q13371, Q2HJA9, Q63737, Q9DBX2, Q9QW08, Q9VUR7, Q9XS39, Q0VCW8, Q4KLJ8, Q5RB77, Q6P268, Q71A38, Q71A39, Q8BVF2, Q9H2J4, Q9Y7L1, Q8MR62, O14530, Q12017, Q32LN3, Q71A37, Q78Y63, Q8K581, Q8N4E4, Q9CQ79, O64628

SIGNOR signaling

5 interactions.

AEffectBMechanism
CSNK2A1up-regulatesPDCLphosphorylation
CSNK2A1unknownPDCLphosphorylation
GRK2“down-regulates activity”PDCLphosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 125 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
Prostacyclin signalling through prostacyclin receptor14109.3×3e-25
G beta:gamma signalling through BTK13107.1×2e-23
G beta:gamma signalling through PLC beta1396.4×8e-23
G beta:gamma signalling through CDC421396.4×8e-23
Presynaptic function of Kainate receptors1391.8×2e-22
ADP signalling through P2Y purinoceptor 121490.3×1e-23
G-protein activation1486.5×2e-23
Thromboxane signalling through TP receptor1486.5×2e-23

GO biological processes:

GO termPartnersFoldFDR
positive regulation of telomere maintenance via telomerase1070.5×2e-14
binding of sperm to zona pellucida728.4×5e-07
protein folding1514.9×1e-11
protein stabilization159.7×6e-09
G protein-coupled receptor signaling pathway155.2×2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance40
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

857 predictions. Top by Δscore:

VariantEffectΔscore
9:122823012:TTA:Tdonor_loss1.0000
9:122823013:TACC:Tdonor_loss1.0000
9:122823014:A:Tdonor_loss1.0000
9:122823015:C:CAdonor_loss1.0000
9:122826611:AGTAC:Adonor_gain1.0000
9:122826614:ACCTG:Adonor_loss1.0000
9:122826788:GGTGT:Gacceptor_gain1.0000
9:122826789:GTGT:Gacceptor_gain1.0000
9:122826790:TGT:Tacceptor_gain1.0000
9:122826791:GT:Gacceptor_gain1.0000
9:122826792:TCTG:Tacceptor_loss1.0000
9:122826793:C:CAacceptor_loss1.0000
9:122826793:C:CCacceptor_gain1.0000
9:122820650:A:Tacceptor_gain0.9900
9:122823018:T:Adonor_gain0.9900
9:122823027:T:Cdonor_gain0.9900
9:122823198:C:CAacceptor_loss0.9900
9:122823198:C:CCacceptor_gain0.9900
9:122823224:C:CTacceptor_gain0.9900
9:122826624:A:Cdonor_gain0.9900
9:122828417:C:CAdonor_gain0.9900
9:122828466:GTTAC:Gdonor_loss0.9900
9:122828467:TTACC:Tdonor_loss0.9900
9:122828468:TAC:Tdonor_loss0.9900
9:122828469:ACC:Adonor_loss0.9900
9:122828470:C:Adonor_loss0.9900
9:122828479:G:Cdonor_gain0.9900
9:122820649:C:CTacceptor_gain0.9800
9:122823225:A:Tacceptor_gain0.9800
9:122826614:A:ACdonor_gain0.9800

AlphaMissense

2031 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:122820560:C:GR144P0.999
9:122823170:C:GR67P0.999
9:122823176:T:AD65V0.999
9:122823189:C:GG61R0.999
9:122823190:T:AK60N0.999
9:122823190:T:GK60N0.999
9:122820188:A:GL268P0.998
9:122820281:A:GL237P0.998
9:122820290:G:CP234R0.998
9:122820290:G:TP234H0.998
9:122820307:G:CF228L0.998
9:122820307:G:TF228L0.998
9:122820308:A:GF228S0.998
9:122820309:A:GF228L0.998
9:122820569:C:GR141P0.998
9:122823160:C:AK70N0.998
9:122823160:C:GK70N0.998
9:122823163:G:CF69L0.998
9:122823163:G:TF69L0.998
9:122823165:A:GF69L0.998
9:122823176:T:CD65G0.998
9:122823176:T:GD65A0.998
9:122823194:G:TP59Q0.998
9:122823197:C:TG58D0.998
9:122820245:A:TV249D0.997
9:122820284:A:GL236P0.997
9:122820287:G:TA235D0.997
9:122820350:A:GF214S0.997
9:122820374:G:TA206D0.997
9:122820375:C:GA206P0.997

dbSNP variants (sampled 300 via entrez): RS1000103836 (9:122818327 A>C), RS1000193961 (9:122830456 T>C), RS1000244984 (9:122818564 T>A), RS1000296201 (9:122824435 G>A), RS1000369487 (9:122827949 T>G), RS1000850464 (9:122820053 C>A,T), RS1000996402 (9:122826322 T>C), RS1001663396 (9:122818063 C>T), RS1001684979 (9:122823477 C>T), RS1002144398 (9:122828807 A>C), RS1002311407 (9:122828972 T>A), RS1003043873 (9:122819194 G>A), RS1003099973 (9:122826565 T>G), RS1003152378 (9:122826266 T>C), RS1003430414 (9:122824823 T>C,G)

Disease associations

OMIM: gene MIM:604421 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001762_547Obesity-related traits5.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004338body weight

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression3
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
bisphenol Faffects cotreatment, increases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
kojic acidincreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
abrinedecreases expression1
Bortezomibincreases expression1
Resveratrolincreases expression, affects cotreatment1
Temozolomideincreases expression1
Leflunomidedecreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diurondecreases expression1
Emodindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Leadincreases expression1
Plant Extractsaffects cotreatment, increases expression1
Smokeincreases abundance, increases expression1
Thiramincreases expression1
Urethaneincreases expression1
1-Methyl-3-isobutylxanthineincreases expression, affects cotreatment1
Copper Sulfateincreases 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.