PRCC

gene
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Also known as RCCP1

Summary

PRCC (proline rich mitotic checkpoint control factor, HGNC:9343) is a protein-coding gene on chromosome 1q23.1, encoding Proline-rich protein PRCC (Q92733). May regulate cell cycle progression through interaction with MAD2L2. It is a selective cancer dependency (DepMap: 20.9% of cell lines).

This gene encodes a protein that may play a role in pre-mRNA splicing. Chromosomal translocations (X;1)(p11;q21) that result in fusion of this gene to TFE3 (GeneID 7030) have been associated with papillary renal cell carcinoma. A PRCC-TFE3 fusion protein is expressed in affected carcinomas and is likely associated with altered gene transactivation. This fusion protein has also been associated with disruption of the cell cycle.

Source: NCBI Gene 5546 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 82 total
  • Phenotypes (HPO): 4
  • Cancer dependency (DepMap): dependent in 20.9% of screened cell lines
  • MANE Select transcript: NM_005973

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9343
Approved symbolPRCC
Nameproline rich mitotic checkpoint control factor
Location1q23.1
Locus typegene with protein product
StatusApproved
AliasesRCCP1
Ensembl geneENSG00000143294
Ensembl biotypeprotein_coding
OMIM179755
Entrez5546

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 21 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000271526, ENST00000454659, ENST00000459707, ENST00000469071, ENST00000473387, ENST00000491853, ENST00000526188, ENST00000888086, ENST00000888087, ENST00000888088, ENST00000888089, ENST00000888090, ENST00000888091, ENST00000888092, ENST00000927762, ENST00000927763, ENST00000927764, ENST00000927765, ENST00000927766, ENST00000927767, ENST00000927768, ENST00000927769, ENST00000950490, ENST00000950491, ENST00000950492

RefSeq mRNA: 1 — MANE Select: NM_005973 NM_005973

CCDS: CCDS1157

Canonical transcript exons

ENST00000271526 — 7 exons

ExonStartEnd
ENSE00000959080156794665156794808
ENSE00000959081156797276156797341
ENSE00001833466156767535156768239
ENSE00001870245156800374156800815
ENSE00003510161156786608156787174
ENSE00003525835156782282156782329
ENSE00003607660156791697156791792

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 96.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 57.7872 / max 357.8567, expressed in 1821 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
577556.81731820
57760.3372152
57770.246883
57710.195399
57740.131031
57730.059710

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534396.92gold quality
ganglionic eminenceUBERON:000402396.53gold quality
ventricular zoneUBERON:000305395.57gold quality
cerebellar hemisphereUBERON:000224595.26gold quality
right hemisphere of cerebellumUBERON:001489095.26gold quality
cerebellar cortexUBERON:000212995.17gold quality
right frontal lobeUBERON:000281094.99gold quality
skin of legUBERON:000151194.95gold quality
right lobe of thyroid glandUBERON:000111994.83gold quality
skin of abdomenUBERON:000141694.82gold quality
hindlimb stylopod muscleUBERON:000425294.82gold quality
gastrocnemiusUBERON:000138894.78gold quality
stromal cell of endometriumCL:000225594.61gold quality
mucosa of transverse colonUBERON:000499194.56gold quality
muscle layer of sigmoid colonUBERON:003580594.35gold quality
left lobe of thyroid glandUBERON:000112094.32gold quality
body of uterusUBERON:000985394.23gold quality
apex of heartUBERON:000209894.20gold quality
lower esophagus mucosaUBERON:003583494.16gold quality
muscle of legUBERON:000138394.14gold quality
granulocyteCL:000009494.11gold quality
right lungUBERON:000216794.10gold quality
endocervixUBERON:000045894.02gold quality
ectocervixUBERON:001224993.96gold quality
lower esophagus muscularis layerUBERON:003583393.93gold quality
left uterine tubeUBERON:000130393.92gold quality
lower esophagusUBERON:001347393.92gold quality
right ovaryUBERON:000211893.85gold quality
esophagogastric junction muscularis propriaUBERON:003584193.83gold quality
prefrontal cortexUBERON:000045193.77gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.79
E-GEOD-110499no253.81
E-MTAB-8060no111.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting PRCC, 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-548C-3P99.9974.017587
HSA-MIR-211099.9666.681930
HSA-MIR-365899.9673.874379
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-130599.9171.433443
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-449299.8768.253611
HSA-MIR-430799.8270.453374
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-378G99.7164.901106
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-64699.6867.841645
HSA-MIR-449999.6267.291470
HSA-MIR-76299.5866.611994
HSA-MIR-449899.4767.422360
HSA-MIR-6852-5P99.1766.692073
HSA-MIR-3160-3P99.0764.78955
HSA-MIR-5001-5P99.0566.761972
HSA-MIR-1207-3P98.9966.221532
HSA-MIR-939-3P98.9765.072347
HSA-MIR-42198.9067.041883
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-7155-5P98.6566.141290
HSA-MIR-615-5P98.1063.76591
HSA-MIR-6742-3P97.9564.501490
HSA-MIR-449497.8664.93850
HSA-MIR-227897.3066.191130
HSA-MIR-1225-3P97.2964.60876

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 20.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • Our data suggest a scenario in which, during the course of renal cell carcinoma development, an initial PRCCTFE3-induced cell cycle delay must be numbed, thus permitting continued proliferation and progression towards full-blown malignancy. (PMID:19422821)
  • results reveal that PRCC-TFE3 dual-fusion FISH probe is an efficient and concise technique for diagnosing PRCC-TFE3 RCC in paraffin-embedded tissue (PMID:28949976)
  • PRCC-TFE3 fusion-mediated PRKN/parkin-dependent mitophagy promotes cell survival and proliferation in PRCC-TFE3 translocation renal cell carcinoma. (PMID:33019842)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioprccENSDARG00000063252
mus_musculusPrccENSMUSG00000004895
rattus_norvegicusPrccENSRNOG00000012933
drosophila_melanogasterCG17249FBGN0035249
caenorhabditis_elegansWBGENE00008034

Protein

Protein identifiers

Proline-rich protein PRCCQ92733 (reviewed: Q92733)

Alternative names: Papillary renal cell carcinoma translocation-associated gene protein

All UniProt accessions (4): Q92733, A0A0S2Z456, H0Y679, H0YE12

UniProt curated annotations — full annotation on UniProt →

Function. May regulate cell cycle progression through interaction with MAD2L2.

Subunit / interactions. Interacts with MAD2L2; the interaction is direct.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous in fetal and adult tissues.

Disease relevance. A chromosomal aberration involving PRCC is found in patients with papillary renal cell carcinoma. Translocation t(X;1)(p11.2;q21.2) with TFE3.

RefSeq proteins (1): NP_005964* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR018800PRCCFamily

Pfam: PF10253

UniProt features (22 total): modified residue 9, compositionally biased region 7, region of interest 4, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92733-F159.890.06

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 (9): 97, 114, 157, 159, 212, 218, 239, 241, 267

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-72163mRNA Splicing - Major Pathway
R-HSA-9918481Dengue Virus-Host Interactions

MSigDB gene sets: 156 (showing top): PATIL_LIVER_CANCER, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_REGULATION_OF_CELL_CYCLE, REACTOME_MRNA_SPLICING, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP, MODULE_18, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24, DURCHDEWALD_SKIN_CARCINOGENESIS_DN, REACTOME_METABOLISM_OF_RNA, TGGAAA_NFAT_Q4_01, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, TCCCRNNRTGC_UNKNOWN

GO Biological Process (1): regulation of cell cycle (GO:0051726)

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

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear speck (GO:0016607)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
mRNA Splicing1
Dengue Virus Infection1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell cycle1
regulation of cellular process1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

1256 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PRCCASPSCR1Q9BZE9967
PRCCTFE3P19532964
PRCCTFEBP19484820
PRCCCLTCQ00610820
PRCCSFPQP23246812
PRCCMAD2L2Q9UI95760
PRCCNONOP30807716
PRCCLUC7L3O95232710
PRCCZNF830Q96NB3696
PRCCCRNKL1Q9BZJ0682
PRCCTBC1D25Q3MII6669
PRCCRBM10P98175658
PRCCHLFQ16534649
PRCCMITFO75030644
PRCCKANSL2Q9H9L4638

IntAct

84 interactions, top by confidence:

ABTypeScore
PRCCNTC20psi-mi:“MI:0915”(physical association)0.560
PRCCHOMER3psi-mi:“MI:0915”(physical association)0.560
EGFRPRCCpsi-mi:“MI:0915”(physical association)0.550
IWS1SUPT5Hpsi-mi:“MI:0914”(association)0.530
PRCCBCAS2psi-mi:“MI:0914”(association)0.530
SYNGAP1IGF2BP3psi-mi:“MI:0914”(association)0.530
SYNGAP1SEC16Apsi-mi:“MI:0914”(association)0.530
FKBP9CASC3psi-mi:“MI:0914”(association)0.530
PLOD3PLOD2psi-mi:“MI:0914”(association)0.530
CSNK2A1PRCCpsi-mi:“MI:0217”(phosphorylation reaction)0.440
PRCCDNAJC10psi-mi:“MI:0915”(physical association)0.400
SF3A2PRCCpsi-mi:“MI:0915”(physical association)0.400
RBM10PRCCpsi-mi:“MI:0915”(physical association)0.370
LSM2PRCCpsi-mi:“MI:0915”(physical association)0.370
PRCCPRPF19psi-mi:“MI:0915”(physical association)0.370
PPIL2PRCCpsi-mi:“MI:0915”(physical association)0.370
PRCCTOE1psi-mi:“MI:0915”(physical association)0.370
CEP170P1PCYT1Apsi-mi:“MI:0914”(association)0.350
Bcas2PEX10psi-mi:“MI:0914”(association)0.350
YWHAZWDR62psi-mi:“MI:0914”(association)0.350
Crnkl1PLRG1psi-mi:“MI:0914”(association)0.350
HSF2RBBP6psi-mi:“MI:0914”(association)0.350
SOD1FAAP20psi-mi:“MI:0914”(association)0.350
LRP8TYK2psi-mi:“MI:0914”(association)0.350

BioGRID (122): PRCC (Affinity Capture-MS), PRCC (Proximity Label-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS), PRCC (Affinity Capture-MS)

ESM2 similar proteins: A4PB26, D3ZTQ1, G1SW77, O16053, O88271, Q12872, Q32LE2, Q3MHS2, Q3U155, Q3USH5, Q4ADK4, Q4ADK7, Q4VAA2, Q5M8L3, Q5PQP2, Q5PQS7, Q5RKH3, Q5VSY0, Q5XHI2, Q5XIG5, Q5XIM5, Q5ZLH9, Q60FC2, Q63ZM9, Q6AXS5, Q6DIS2, Q6DJ13, Q6GNQ4, Q6NWC9, Q6PFK1, Q75UQ2, Q7T370, Q7ZYA6, Q8HXY9, Q8K039, Q8MMC4, Q8NC51, Q8R1N0, Q92733, Q96NB3

SIGNOR signaling

1 interactions.

AEffectBMechanism
PRCCup-regulatesMAD2L2relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 104 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
mRNA 3’-end processing718.9×4e-06
Transport of Mature mRNA derived from an Intron-Containing Transcript816.7×1e-06
mRNA Splicing1116.6×4e-09
Processing of Capped Intron-Containing Pre-mRNA1415.8×3e-11
mRNA Splicing - Minor Pathway515.3×8e-04
RNA Polymerase II Transcription Termination515.0×8e-04
mRNA Splicing - Major Pathway2015.0×6e-16
mRNA Polyadenylation1214.4×3e-09

GO biological processes:

GO termPartnersFoldFDR
mRNA transport719.4×2e-05
mRNA splicing, via spliceosome1716.4×2e-13
negative regulation of translation612.4×1e-03
mRNA processing129.9×1e-06
RNA splicing98.4×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance57
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1399 predictions. Top by Δscore:

VariantEffectΔscore
1:156782276:TCTTA:Tacceptor_loss1.0000
1:156782277:CTTA:Cacceptor_loss1.0000
1:156782278:TTAG:Tacceptor_loss1.0000
1:156782279:TA:Tacceptor_loss1.0000
1:156782280:A:AGacceptor_gain1.0000
1:156782280:AGT:Aacceptor_loss1.0000
1:156782281:G:Cacceptor_loss1.0000
1:156782281:G:GAacceptor_gain1.0000
1:156782281:GTC:Gacceptor_gain1.0000
1:156782281:GTCA:Gacceptor_gain1.0000
1:156782330:GTAAG:Gdonor_loss1.0000
1:156782331:T:Adonor_loss1.0000
1:156786587:T:Gacceptor_gain1.0000
1:156786593:A:AGacceptor_gain1.0000
1:156786593:ACCT:Aacceptor_gain1.0000
1:156786593:ACCTG:Aacceptor_gain1.0000
1:156786596:T:TAacceptor_gain1.0000
1:156791790:GCA:Gdonor_gain1.0000
1:156791793:G:GGdonor_gain1.0000
1:156791798:T:Gdonor_gain1.0000
1:156794659:TTCCA:Tacceptor_gain1.0000
1:156794660:TCCAG:Tacceptor_gain1.0000
1:156794661:CCA:Cacceptor_gain1.0000
1:156794662:CAG:Cacceptor_gain1.0000
1:156794663:A:AGacceptor_gain1.0000
1:156794663:AG:Aacceptor_gain1.0000
1:156794664:G:Aacceptor_gain1.0000
1:156794664:G:GTacceptor_gain1.0000
1:156794664:GT:Gacceptor_gain1.0000
1:156794664:GTT:Gacceptor_gain1.0000

AlphaMissense

3159 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:156786825:T:AI245N1.000
1:156786837:C:AA249D1.000
1:156797292:C:AP447Q1.000
1:156797307:G:CR452P1.000
1:156797310:G:CR453P1.000
1:156797312:A:GK454E1.000
1:156797313:A:TK454I1.000
1:156797314:A:CK454N1.000
1:156797314:A:TK454N1.000
1:156797315:C:GH455D1.000
1:156797316:A:CH455P1.000
1:156797317:C:AH455Q1.000
1:156797317:C:GH455Q1.000
1:156797319:A:CQ456P1.000
1:156797322:T:AI457N1.000
1:156797322:T:CI457T1.000
1:156797322:T:GI457S1.000
1:156797327:T:AY459N1.000
1:156797327:T:CY459H1.000
1:156797327:T:GY459D1.000
1:156797331:T:AL460H1.000
1:156797331:T:CL460P1.000
1:156797331:T:GL460R1.000
1:156797334:T:AI461N1.000
1:156797336:C:GH462D1.000
1:156797337:A:CH462P1.000
1:156797340:A:CQ463P1.000
1:156800374:G:CA464P1.000
1:156800375:C:AA464D1.000
1:156800384:G:CR467P1.000

dbSNP variants (sampled 300 via entrez): RS1000093462 (1:156799626 T>C), RS1000155101 (1:156785598 A>G,T), RS1000176720 (1:156786447 C>T), RS1000357472 (1:156793235 G>C), RS1000371192 (1:156792899 C>T), RS1000460168 (1:156786137 A>G), RS1000473839 (1:156773842 A>G), RS1000536870 (1:156766750 C>T), RS1000626471 (1:156780161 G>A,C), RS1000762210 (1:156787452 T>C,G), RS1000847451 (1:156774126 G>A,C), RS1000968408 (1:156791302 C>T), RS1000997257 (1:156767133 G>A), RS1001089561 (1:156787743 C>T), RS1001098141 (1:156798238 T>C)

Disease associations

OMIM: gene MIM:179755 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (1): Hereditary papillary renal cell carcinoma (Orphanet:47044)

HPO phenotypes

4 total (4 of 4 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0001442Typified by somatic mosaicism
HP:0003829Typified by incomplete penetrance
HP:0006766Papillary renal cell carcinoma

GWAS associations

1 associations (top):

StudyTraitp-value
GCST004061_1Sjögren’s syndrome2.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
methylmercuric chlorideincreases expression, affects cotreatment2
Cadmium Chlorideincreases abundance, decreases expression2
FR900359affects phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
pirinixic acidincreases expression, affects binding, increases activity1
bisphenol Aaffects cotreatment, increases methylation1
sodium arsenitedecreases expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
nutlin 3affects cotreatment, increases secretion1
ICG 001decreases expression1
dorsomorphinaffects cotreatment, increases 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
Resveratrolaffects cotreatment, decreases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Fulvestrantaffects cotreatment, increases methylation1
Leflunomidedecreases expression1
Vehicle Emissionsincreases abundance, increases expression1
Cadmiumdecreases expression, increases abundance1
Caffeineincreases phosphorylation1
Dactinomycinaffects cotreatment, increases secretion1
Doxorubicindecreases expression1
Ketoconazoleincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Quercetinincreases phosphorylation1
Urethaneincreases expression1
Valproic Acidincreases expression1
Aflatoxin B1increases methylation1

Cellosaurus cell lines

6 cell lines: 5 cancer cell line, 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B099UOK120Cancer cell lineMale
CVCL_B105UOK124Cancer cell lineFemale
CVCL_B123UOK146Cancer cell lineFemale
CVCL_B3EQAbcam HEK293T PRCC KOTransformed cell lineFemale
CVCL_WY83CL89-12117Cancer cell lineMale
CVCL_WY84CL89-17872Cancer cell lineMale

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): Sjogren syndrome