PRR11

Summary

PRR11 (proline rich 11, HGNC:25619) is a protein-coding gene on chromosome 17q22, encoding Proline-rich protein 11 (Q96HE9). Plays a critical role in cell cycle progression.

Involved in regulation of cell cycle. Located in cytoplasm and nucleus.

Source: NCBI Gene 55771 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_018304

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25619
Approved symbol	PRR11
Name	proline rich 11
Location	17q22
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11029
Ensembl gene	ENSG00000068489
Ensembl biotype	protein_coding
OMIM	615920
Entrez	55771

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000262293, ENST00000577457, ENST00000578542, ENST00000578777, ENST00000580177, ENST00000581182, ENST00000582004, ENST00000582995, ENST00000614081

RefSeq mRNA: 1 — MANE Select: NM_018304 NM_018304

CCDS: CCDS11614

Canonical transcript exons

ENST00000262293 — 10 exons

Exon	Start	End
ENSE00000739668	59185440	59185562
ENSE00001113052	59197544	59197603
ENSE00001113053	59194757	59194855
ENSE00001113061	59195331	59195443
ENSE00001325603	59201563	59206709
ENSE00001329233	59193492	59193734
ENSE00001329988	59185054	59185204
ENSE00003482503	59197693	59197789
ENSE00003526782	59169748	59169880
ENSE00003901017	59155746	59155805

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 99.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.5758 / max 227.4910, expressed in 1644 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161947	18.7574	1481
161946	2.6526	1065
161945	1.8578	959
161944	0.3079	174

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	99.90	gold quality
renal medulla	UBERON:0000362	99.78	gold quality
cardia of stomach	UBERON:0001162	99.75	gold quality
pylorus	UBERON:0001166	99.71	gold quality
nipple	UBERON:0002030	99.69	gold quality
superior surface of tongue	UBERON:0007371	99.69	gold quality
buccal mucosa cell	CL:0002336	99.67	gold quality
trigeminal ganglion	UBERON:0001675	99.67	gold quality
ventral tegmental area	UBERON:0002691	99.67	gold quality
inferior vagus X ganglion	UBERON:0005363	99.62	gold quality
superior vestibular nucleus	UBERON:0007227	99.61	gold quality
subthalamic nucleus	UBERON:0001906	99.57	gold quality
dorsal root ganglion	UBERON:0000044	99.56	gold quality
sperm	CL:0000019	99.55	gold quality
visceral pleura	UBERON:0002401	99.46	gold quality
substantia nigra pars compacta	UBERON:0001965	99.45	gold quality
pericardium	UBERON:0002407	99.45	gold quality
substantia nigra pars reticulata	UBERON:0001966	99.40	gold quality
lateral globus pallidus	UBERON:0002476	99.39	gold quality
pons	UBERON:0000988	99.38	gold quality
saphenous vein	UBERON:0007318	99.36	gold quality
pharyngeal mucosa	UBERON:0000355	99.33	gold quality
urethra	UBERON:0000057	99.32	gold quality
mucosa of paranasal sinus	UBERON:0005030	99.31	gold quality
superficial temporal artery	UBERON:0001614	99.20	gold quality
penis	UBERON:0000989	99.19	gold quality
body of tongue	UBERON:0011876	99.19	gold quality
synovial joint	UBERON:0002217	99.11	gold quality
parietal pleura	UBERON:0002400	99.11	gold quality
male germ cell	CL:0000015	99.09	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-7051	yes	571.38
E-GEOD-99795	yes	76.54
E-MTAB-6678	yes	9.63
E-ANND-3	yes	5.91
E-CURD-53	no	567.84
E-MTAB-8559	no	432.56
E-MTAB-8205	no	239.96

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F4

miRNA regulators (miRDB)

221 targeting PRR11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753

Literature-anchored findings (GeneRIF, showing 28)

• the apparent occurrence of an unusual TG 3’ splice site in intron 10 is discussed (PMID:17672918)
• our results strongly demonstrated that this newly identified gene, PRR11, had a critical role in both cell cycle progression and tumorigenesis, and might serve as a novel potential target in the diagnosis and/or treatment of human lung cancer. (PMID:23246489)
• Overexpression of PRR11 inhibits cell proliferation and induces premature chromatin condensation. (PMID:25666944)
• Microarray analysis revealed that several genes involved in cell proliferation, cell adhesion, and cell migration were altered in PRR11-knockout cells. (PMID:25971332)
• Targeted depletion of PRR11 caused a dramatic cell cycle arrest followed by massive apoptotic cell death, and eventually resulted in a significant decrease in growth and viability in lung cancer cell lines. (PMID:25973065)
• PRR11-SKA2 bidirectional transcription unit, which is a novel direct target of NF-Y, is essential for the accelerated proliferation and motility of lung cancer cells (PMID:26162986)
• PRR11 may be widely activated in human gastric cancer. (PMID:26252227)
• p53 negatively regulates the expression of the PRR11-SKA2 bidirectional transcription unit through NF-Y, suggesting that the inability to repress the PRR11-SKA2 bidirectional transcription unit after loss of p53 might contribute to tumorigenesis. (PMID:28257042)
• these findings indicated that miR-144-3p induced cell cycle arrest and apoptosis in pancreatic cancer by targeting PRR11. (PMID:28574724)
• these findings further illustrate the suppressive role of miR-195 in prostate cancer (PCa), and indicate a novel role of PRR11 in PCa. Importantly, the newly identified miR-195/PRR11 axis may aid with identifying potential therapeutic targets in PCa. (PMID:29393495)
• PRR11 regulated self-renewal and tumorigenicity of gastric cancer stem cells through MAPK signaling, and could be used as a therapeutic target for gastric cancer. (PMID:30007956)
• PRR11 positively regulated cell proliferation-related proteins, including c-myc and cyclin D1, and increased and decreased the expression of matrix metalloproteinase 2 and tissue inhibitor of metalloproteinase 2 and PRR11 expression was mediated by the phosphoinositide 3-kinase/AKT/beta-catenin signaling pathway. (PMID:30165366)
• PRR11 plays an oncogenic role in hepatocellular carcinoma (HCC) progression, through activating the Wnt/beta-catenin signaling pathway, and may represent a valuable prognostic marker and therapeutic target for HCC. (PMID:30248355)
• Knockdown of DLX6-AS1 inhibited cell proliferation, migration, invasion and promoted apoptosis by downregulating PRR11 expression and upregulating miR-144 in NSCLC. (PMID:30551440)
• MicroRNA-211-5p promotes apoptosis and inhibits the migration of osteosarcoma cells by targeting proline-rich protein PRR11. (PMID:31075210)
• Proline-rich 11 (PRR11) drives F-actin assembly by recruiting the actin-related protein 2/3 complex in human non-small cell lung carcinoma. (PMID:32169900)
• Proline rich 11 (PRR11) overexpression amplifies PI3K signaling and promotes antiestrogen resistance in breast cancer. (PMID:33127913)
• HEDGEHOG/GLI Modulates the PRR11-SKA2 Bidirectional Transcription Unit in Lung Squamous Cell Carcinomas. (PMID:33477943)
• PRR11 unveiled as a top candidate biomarker within the RBM3-regulated transcriptome in pancreatic cancer. (PMID:34379360)
• MicroRNA-26b-5p suppresses the proliferation of tongue squamous cell carcinoma via targeting proline rich 11 (PRR11). (PMID:34488538)
• PRR11 promotes ccRCC tumorigenesis by regulating E2F1 stability. (PMID:34499617)
• PRR11 Promotes Proliferation and Migration of Colorectal Cancer through Activating the EGFR/ERK/AKT Pathway via Increasing CTHRC1. (PMID:35181621)
• Proline-rich 11 (PRR11) promotes the progression of cutaneous squamous cell carcinoma by activating the EGFR signaling pathway. (PMID:36727626)
• Clinical significance and effect of PRR 11 up-regulation on the malignancy of osteosarcoma. (PMID:36734441)
• PRR11 is a prognostic biomarker and correlates with immune infiltrates in bladder urothelial carcinoma. (PMID:36739300)
• Predictive significance of PRR11 in prognosis and immune infiltration of glioma patients. (PMID:37036189)
• ELF1/PRR11/ARP2/3 promoted trophoblast cells proliferation and motility in early pregnancy. (PMID:37641376)
• Prognostic value of PRR11 and immune cell infiltration in Ewing sarcoma. (PMID:38427643)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	prr11	ENSDARG00000087393
mus_musculus	Prr11	ENSMUSG00000020493
rattus_norvegicus	Prr11	ENSRNOG00000006198

Paralogs (2): JMY (ENSG00000152409), WHAMM (ENSG00000156232)

Protein

Protein identifiers

Proline-rich protein 11 — Q96HE9 (reviewed: Q96HE9)

All UniProt accessions (6): Q96HE9, D2SNZ4, J3QKY4, J3QQS2, J3QR53, J3QRV0

UniProt curated annotations — full annotation on UniProt →

Function. Plays a critical role in cell cycle progression.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Ubiquitously expressed.

Post-translational modifications. Ubiquitinated. Rapidly degraded by the proteasome; degradation may involve FBXW7-specific phosphorylated phosphodegron motifs.

Induction. Expression increases from G1 to G2/M phase.

RefSeq proteins (1): NP_060774* (*=MANE)

Domains & families (InterPro)

UniProt features (18 total): modified residue 7, short sequence motif 4, region of interest 3, compositionally biased region 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96HE9-F1	66.84	0.10

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 (7): 33, 40, 287, 291, 344, 346, 348

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 235 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, HORIUCHI_WTAP_TARGETS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, CAGCTG_AP4_Q5, SHEPARD_BMYB_MORPHOLINO_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, MYOD_01, GOBP_REGULATION_OF_CELL_CYCLE, LIAO_METASTASIS, TGACATY_UNKNOWN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, BENPORATH_NOS_TARGETS, FISCHER_DREAM_TARGETS, IK3_01, PIT1_Q6

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

GO Molecular Function (0):

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cell cycle	1
regulation of cellular process	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

740 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRR11	SKA2	Q8WVK7	580
PRR11	BLTP2	Q14667	390
PRR11	ZNF721	Q8TF20	349
PRR11	PCIF1	Q9H4Z3	336
PRR11	PRR12	Q9ULL5	324
PRR11	ACTR2	P61160	312
PRR11	PBX3	P40426	298
PRR11	ANKIB1	Q9P2G1	294
PRR11	ICA1L	Q8NDH6	284
PRR11	FBLIM1	Q8WUP2	284
PRR11	KRABD5	Q7Z2F6	278
PRR11	CYP20A1	Q6UW02	272
PRR11	GK5	Q6ZS86	271
PRR11	CCNA1	P78396	270
PRR11	SKA3	Q8IX90	269

IntAct

39 interactions, top by confidence:

A	B	Type	Score
OSBPL5	NAGLU	psi-mi:“MI:0914”(association)	0.640
PRR11	NVL	psi-mi:“MI:0914”(association)	0.530
IL4R	RHOBTB3	psi-mi:“MI:0914”(association)	0.530
RPL13	RRP8	psi-mi:“MI:0914”(association)	0.530
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
IL4R	DHRS3	psi-mi:“MI:0914”(association)	0.350
rep	AP3B1	psi-mi:“MI:0914”(association)	0.350
MYC		psi-mi:“MI:0914”(association)	0.350
ACTG1	ENAH	psi-mi:“MI:0914”(association)	0.350
CALD1		psi-mi:“MI:0914”(association)	0.350
KCNA2	TMEM129	psi-mi:“MI:0914”(association)	0.350
TTMP	TMEM223	psi-mi:“MI:0914”(association)	0.350
PIPSL	C1orf226	psi-mi:“MI:0914”(association)	0.350
FTL	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
TGFA	TNPO2	psi-mi:“MI:0914”(association)	0.350
TNFRSF1B	MAP3K7	psi-mi:“MI:0914”(association)	0.350
PRR11	ARHGAP1	psi-mi:“MI:0914”(association)	0.350
CAVIN1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
FTL		psi-mi:“MI:0914”(association)	0.350
HMGA1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
LIN28A	GTPBP10	psi-mi:“MI:0914”(association)	0.350
LYAR	PES1	psi-mi:“MI:0914”(association)	0.350
MEAF6	WDR46	psi-mi:“MI:0914”(association)	0.350
MORF4L2	GTPBP10	psi-mi:“MI:0914”(association)	0.350

BioGRID (245): NIP7 (Affinity Capture-MS), KNOP1 (Affinity Capture-MS), RBM28 (Affinity Capture-MS), SF3B1 (Affinity Capture-MS), POP1 (Affinity Capture-MS), DDX24 (Affinity Capture-MS), FTSJ3 (Affinity Capture-MS), SF3B2 (Affinity Capture-MS), ZNF668 (Affinity Capture-MS), RPL3 (Affinity Capture-MS), UPF1 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), RPL10A (Affinity Capture-MS), DKC1 (Affinity Capture-MS), PABPC4 (Affinity Capture-MS)

ESM2 similar proteins: A4IG59, A7Z063, A8K0Z3, A8MWX3, B0K035, B2RYF7, C4AMC7, E7F568, F1RCE7, G3V9A7, P57095, Q03173, Q08AE8, Q08BD8, Q1LYM3, Q28DN4, Q3KQW7, Q3ZBW7, Q4R707, Q52KF3, Q58CR1, Q5R3Z9, Q5R789, Q5RIX9, Q5RKG1, Q5U4A3, Q5XII9, Q5ZKA6, Q64GL0, Q6DD45, Q6DFB7, Q6NZY4, Q6P444, Q6VEQ5, Q7T3E8, Q801E2, Q8BHE0, Q8BHS8, Q8VDD8, Q8VED8

Diamond homologs: Q8BHE0, Q96HE9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 54 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:

Pathway	Partners	Fold	FDR
Eukaryotic Translation Initiation	5	39.6×	3e-06
Cap-dependent Translation Initiation	5	39.6×	3e-06
SARS-CoV-1 modulates host translation machinery	5	39.6×	3e-06
Eukaryotic Translation Elongation	5	35.7×	4e-06
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	5	34.9×	5e-06
Nonsense-Mediated Decay (NMD)	5	29.9×	1e-05
SARS-CoV-2 modulates host translation machinery	5	28.7×	1e-05
Influenza Viral RNA Transcription and Replication	5	27.6×	1e-05

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	7	27.6×	2e-06
ribosomal small subunit biogenesis	5	24.2×	2e-04
rRNA processing	7	21.1×	8e-06
translation	7	15.3×	5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1317 predictions. Top by Δscore:

Variant	Effect	Δscore
17:59155801:GACTA:G	donor_gain	1.0000
17:59155802:ACTA:A	donor_gain	1.0000
17:59155803:CTA:C	donor_gain	1.0000
17:59155804:TAG:T	donor_loss	1.0000
17:59155805:AG:A	donor_loss	1.0000
17:59155806:G:GG	donor_gain	1.0000
17:59169746:A:AG	acceptor_gain	1.0000
17:59169747:G:GG	acceptor_gain	1.0000
17:59169747:GAA:G	acceptor_gain	1.0000
17:59169876:GAAAG:G	donor_gain	1.0000
17:59194755:A:G	acceptor_gain	1.0000
17:59195444:G:GG	donor_gain	1.0000
17:59197542:A:AG	acceptor_gain	1.0000
17:59197543:G:GG	acceptor_gain	1.0000
17:59197543:GC:G	acceptor_gain	1.0000
17:59197543:GCA:G	acceptor_gain	1.0000
17:59197769:GCCT:G	donor_gain	1.0000
17:59155804:TA:T	donor_gain	0.9900
17:59155807:T:G	donor_loss	0.9900
17:59155816:G:GT	donor_gain	0.9900
17:59155817:A:T	donor_gain	0.9900
17:59157336:A:AG	donor_gain	0.9900
17:59169742:CTGCA:C	acceptor_loss	0.9900
17:59169743:TGCAG:T	acceptor_loss	0.9900
17:59169744:GCA:G	acceptor_loss	0.9900
17:59169745:CA:C	acceptor_loss	0.9900
17:59169746:A:AT	acceptor_loss	0.9900
17:59169747:GA:G	acceptor_gain	0.9900
17:59169747:GAAAT:G	acceptor_gain	0.9900
17:59169879:AGG:A	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000025106 (17:59160834 C>T), RS1000067031 (17:59175965 A>C,G), RS1000079762 (17:59191649 C>G), RS1000309334 (17:59158373 G>A), RS1000359436 (17:59207179 G>A), RS1000474033 (17:59201635 C>G), RS1000538034 (17:59168403 C>G,T), RS1000592559 (17:59201989 A>C,G,T), RS1000609564 (17:59201256 C>T), RS1000766137 (17:59196034 G>A), RS1000793901 (17:59206779 C>T), RS1000838193 (17:59181884 G>A), RS1000869374 (17:59181651 G>A,C), RS1000905508 (17:59188652 C>G,T), RS1000910671 (17:59163142 G>C)

Disease associations

OMIM: gene MIM:615920 | 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

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

Chemical	Actions (top 5)	PubMed papers
Cadmium	decreases expression, increases abundance	2
Doxorubicin	decreases expression	2
Cyclosporine	decreases expression	2
Cadmium Chloride	increases expression, decreases expression, increases abundance	2
aristolochic acid I	increases expression	1
FR900359	affects phosphorylation	1
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
propionaldehyde	decreases expression	1
bisphenol A	decreases expression	1
lead acetate	affects cotreatment, increases expression	1
zinc protoporphyrin	affects cotreatment, increases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
coumarin	increases phosphorylation	1
diallyl trisulfide	decreases expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
azoxystrobin	increases expression	1
CGP 52608	increases reaction, affects binding	1
deguelin	increases expression	1
2-palmitoylglycerol	increases expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
pyrimidifen	increases expression	1
thifluzamide	increases expression	1
abrine	decreases expression	1
palbociclib	decreases expression	1
pyrachlostrobin	increases expression	1
jinfukang	increases expression	1

Clinical trials (associated diseases)

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