PRR13

Summary

PRR13 (proline rich 13, HGNC:24528) is a protein-coding gene on chromosome 12q13.13, encoding Proline-rich protein 13 (Q9NZ81). Negatively regulates TSP1 expression at the level of transcription. It is a selective cancer dependency (DepMap: 36.3% of cell lines).

Located in cytosol and nucleoplasm.

Source: NCBI Gene 54458 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 23 total
• Cancer dependency (DepMap): dependent in 36.3% of screened cell lines
• MANE Select transcript: NM_018457

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24528
Approved symbol	PRR13
Name	proline rich 13
Location	12q13.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23818, DKFZP564J157
Ensembl gene	ENSG00000205352
Ensembl biotype	protein_coding
OMIM	610459
Entrez	54458

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 33 protein_coding, 2 retained_intron

ENST00000379786, ENST00000429243, ENST00000546581, ENST00000547368, ENST00000549068, ENST00000549135, ENST00000549581, ENST00000549740, ENST00000549924, ENST00000551003, ENST00000551365, ENST00000551945, ENST00000552846, ENST00000860096, ENST00000860097, ENST00000860098, ENST00000860099, ENST00000860100, ENST00000860101, ENST00000860102, ENST00000860103, ENST00000860104, ENST00000860105, ENST00000939162, ENST00000939163, ENST00000939164, ENST00000939165, ENST00000939166, ENST00000939167, ENST00000939168, ENST00000939169, ENST00000939170, ENST00000939171, ENST00000939172, ENST00000964979

RefSeq mRNA: 2 — MANE Select: NM_018457 NM_001005354, NM_018457

CCDS: CCDS31811, CCDS44899

Canonical transcript exons

ENST00000429243 — 4 exons

Exon	Start	End
ENSE00001482499	53441734	53441792
ENSE00002325671	53446015	53446638
ENSE00003591931	53442695	53442733
ENSE00003606245	53443391	53443773

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 93.2834 / max 1226.5717, expressed in 1828 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125762	74.8221	1825
125763	12.6017	1786
125761	2.2419	1420
125760	1.4519	534
125758	0.8501	308
125757	0.5306	206
125759	0.5196	151
125764	0.2034	96
125765	0.0621	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	99.48	gold quality
duodenum	UBERON:0002114	99.39	gold quality
adult mammalian kidney	UBERON:0000082	99.32	gold quality
granulocyte	CL:0000094	99.31	gold quality
blood	UBERON:0000178	99.21	gold quality
metanephros cortex	UBERON:0010533	99.12	gold quality
small intestine	UBERON:0002108	99.07	gold quality
small intestine Peyer’s patch	UBERON:0003454	99.07	gold quality
rectum	UBERON:0001052	99.06	gold quality
cortex of kidney	UBERON:0001225	98.96	gold quality
leukocyte	CL:0000738	98.94	gold quality
bone marrow cell	CL:0002092	98.94	gold quality
transverse colon	UBERON:0001157	98.91	gold quality
monocyte	CL:0000576	98.90	gold quality
body of stomach	UBERON:0001161	98.90	gold quality
colonic epithelium	UBERON:0000397	98.86	gold quality
bone marrow	UBERON:0002371	98.82	gold quality
vermiform appendix	UBERON:0001154	98.78	gold quality
spleen	UBERON:0002106	98.78	gold quality
gall bladder	UBERON:0002110	98.78	gold quality
lymph node	UBERON:0000029	98.76	gold quality
right adrenal gland	UBERON:0001233	98.76	gold quality
right adrenal gland cortex	UBERON:0035827	98.71	gold quality
left adrenal gland	UBERON:0001234	98.64	gold quality
mucosa of stomach	UBERON:0001199	98.60	gold quality
right lung	UBERON:0002167	98.58	gold quality
islet of Langerhans	UBERON:0000006	98.57	gold quality
right uterine tube	UBERON:0001302	98.56	gold quality
fundus of stomach	UBERON:0001160	98.53	gold quality
left adrenal gland cortex	UBERON:0035825	98.53	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	65.68
E-MTAB-10042	yes	16.96
E-MTAB-8410	yes	15.70
E-MTAB-9388	yes	13.53
E-ENAD-17	no	4237.16
E-MTAB-6058	no	109.43
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

42 targeting PRR13, 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-12118	100.00	65.88	1270
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-12117	99.50	67.57	868
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-100-3P	99.20	67.33	672
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-942-3P	98.81	69.04	876
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-676-5P	98.49	68.87	1492
HSA-MIR-6801-3P	98.04	64.64	805
HSA-MIR-4468	98.01	66.85	1187
HSA-MIR-6810-3P	97.96	64.57	1023

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 36.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 5)

• Multivariate analysis showed that high TXR1/low TSP1 expression was an independent prognostic factor for decreased median time to tumor progression (TTP) and median overall survival (mOS). (PMID:19435835)
• Low TXR1 mRNA levels were associated with higher response rate (RR), longer median progression-free survival (PFS) and median overall survival (mOS), whereas high TSP1 expression was correlated with higher RR, longer PFS and mOS (PMID:21157449)
• High Txr1 expression is associated with oxaliplatin resistance in gastric cancer. (PMID:24362794)
• These findings indicate that PRR13/THBS1 and TXN expression could be used for the prediction of resistance to treatment of epithelial ovarian cancer patients. (PMID:27779244)
• In primary glioblastoma samples there was a high expression of TXR1 in cerebral tissue compared to control tissue. (PMID:28345125)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Proline-rich protein 13 — Q9NZ81 (reviewed: Q9NZ81)

Alternative names: Taxane-resistance protein

All UniProt accessions (7): Q9NZ81, F8VP70, F8VRX0, F8VU40, F8VWB5, F8VZP4, F8W1R5

UniProt curated annotations — full annotation on UniProt →

Function. Negatively regulates TSP1 expression at the level of transcription. This down-regulation was shown to reduce taxane-induced apoptosis.

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NZ81-1	1	yes
Q9NZ81-2	2

RefSeq proteins (2): NP_001005354, NP_060927* (*=MANE)

Domains & families (InterPro)

UniProt features (10 total): compositionally biased region 4, sequence conflict 3, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NZ81-F1	65.92	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 186 (showing top): MARTINEZ_RB1_TARGETS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP, GRUETZMANN_PANCREATIC_CANCER_UP, BURTON_ADIPOGENESIS_8, MARTINEZ_RB1_AND_TP53_TARGETS_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, MARSON_BOUND_BY_FOXP3_STIMULATED, CHEN_METABOLIC_SYNDROM_NETWORK, REN_ALVEOLAR_RHABDOMYOSARCOMA_DN, LI_INDUCED_T_TO_NATURAL_KILLER_UP, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS, RAO_BOUND_BY_SALL4_ISOFORM_B, LIM_MAMMARY_STEM_CELL_DN, GSE13522_WT_VS_IFNAR_KO_SKIN_DN

GO Biological Process (0):

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

GO Cellular Component (3): nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
nuclear lumen	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

918 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRR13	CD47	Q08722	726
PRR13	THBS1	P07996	667
PRR13	DUSP1	P28562	548
PRR13	ITGA9	Q13797	547
PRR13	THBS2	P35442	529
PRR13	TYMP	P19971	497
PRR13	ASCC1	Q8N9N2	408
PRR13	WDR86	Q86TI4	391
PRR13	ID1	P41134	390
PRR13	PXN	P49023	389
PRR13	THBS3	P49746	388
PRR13	P2RY4	P51582	359
PRR13	ETV3L	Q6ZN32	352
PRR13	UPK3BL1	B0FP48	348
PRR13	ITGB1	P05556	342

IntAct

185 interactions, top by confidence:

A	B	Type	Score
PRR13	KLHL12	psi-mi:“MI:0915”(physical association)	0.780
SDCBP2	PRR13	psi-mi:“MI:0915”(physical association)	0.780
KLHL12	PRR13	psi-mi:“MI:0915”(physical association)	0.780
PRR13	SDCBP2	psi-mi:“MI:0915”(physical association)	0.780
TNFAIP8	PRR13	psi-mi:“MI:0915”(physical association)	0.720
PRR13	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.720
PRR13	PSME3	psi-mi:“MI:0915”(physical association)	0.720
VAC14	PRR13	psi-mi:“MI:0915”(physical association)	0.720
PSME3	PRR13	psi-mi:“MI:0915”(physical association)	0.720
PRR13	VAC14	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-8	PRR13	psi-mi:“MI:0915”(physical association)	0.720
PRR13	TNFAIP8	psi-mi:“MI:0915”(physical association)	0.720
ZCCHC10	PRR13	psi-mi:“MI:0915”(physical association)	0.670
PRR13	LGALS3	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (64): PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), PRR13 (Two-hybrid), ZCCHC10 (Two-hybrid), VAC14 (Two-hybrid), KLHL12 (Two-hybrid)

ESM2 similar proteins: A0A2H4S6M4, A2XT03, C0HM81, C9JFL3, J4WMI6, O31510, O94426, P02810, P04474, P04706, P06600, P06680, P08297, P10163, P10165, P16329, P17816, P19470, P21749, P37705, P50439, P54643, P86960, Q00451, Q00725, Q01642, Q01643, Q01644, Q01645, Q04118, Q0WV37, Q20689, Q25055, Q27270, Q32L04, Q5U1W2, Q61900, Q62266, Q62267, Q63532

Diamond homologs: Q5U1W2, Q9CQJ5, Q9NZ81

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 50 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
Keratinization	11	17.5×	4e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

857 predictions. Top by Δscore:

Variant	Effect	Δscore
12:53442693:A:AG	acceptor_gain	0.9900
12:53442694:G:GG	acceptor_gain	0.9900
12:53442734:G:GG	donor_gain	0.9900
12:53443619:C:A	acceptor_gain	0.9900
12:53443663:AT:A	acceptor_gain	0.9900
12:53443770:CAAG:C	donor_loss	0.9900
12:53443771:AAG:A	donor_loss	0.9900
12:53443773:GGT:G	donor_loss	0.9900
12:53443774:G:T	donor_loss	0.9900
12:53443775:T:A	donor_loss	0.9900
12:53446013:A:AG	acceptor_gain	0.9900
12:53446014:G:GG	acceptor_gain	0.9900
12:53441786:TGGAA:T	donor_gain	0.9800
12:53442690:CTCAG:C	acceptor_loss	0.9800
12:53442693:AGGCT:A	acceptor_gain	0.9800
12:53442694:GGCT:G	acceptor_gain	0.9800
12:53442694:GGCTG:G	acceptor_gain	0.9800
12:53443643:T:TA	acceptor_gain	0.9800
12:53443652:T:A	acceptor_gain	0.9800
12:53446014:GC:G	acceptor_gain	0.9800
12:53443612:T:G	acceptor_gain	0.9700
12:53443613:A:AG	acceptor_gain	0.9700
12:53443614:C:G	acceptor_gain	0.9700
12:53443659:T:TA	acceptor_gain	0.9700
12:53443664:T:TA	acceptor_gain	0.9700
12:53445900:G:T	acceptor_gain	0.9700
12:53446014:GCA:G	acceptor_gain	0.9700
12:53441789:A:T	donor_gain	0.9600
12:53442693:AG:A	acceptor_gain	0.9600
12:53442694:GG:G	acceptor_gain	0.9600

AlphaMissense

967 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:53446042:A:C	S144R	0.946
12:53446044:C:A	S144R	0.946
12:53446044:C:G	S144R	0.946
12:53443713:G:C	K114N	0.938
12:53443713:G:T	K114N	0.938
12:53443725:A:C	K118N	0.934
12:53443725:A:T	K118N	0.934
12:53443724:A:T	K118I	0.931
12:53446045:A:C	S145R	0.918
12:53446047:T:A	S145R	0.918
12:53446047:T:G	S145R	0.918
12:53443704:G:C	K111N	0.908
12:53443704:G:T	K111N	0.908
12:53443692:G:C	K107N	0.902
12:53443692:G:T	K107N	0.902
12:53443715:A:T	K115I	0.881
12:53443703:A:C	K111T	0.875
12:53443712:A:C	K114T	0.872
12:53443695:G:C	K108N	0.860
12:53443695:G:T	K108N	0.860
12:53443724:A:C	K118T	0.853
12:53443531:T:C	F54L	0.842
12:53443533:C:A	F54L	0.842
12:53443533:C:G	F54L	0.842
12:53443691:A:T	K107M	0.842
12:53443712:A:T	K114M	0.842
12:53443716:A:C	K115N	0.840
12:53443716:A:T	K115N	0.840
12:53443707:A:C	K112N	0.835
12:53443707:A:T	K112N	0.835

dbSNP variants (sampled 300 via entrez): RS1000542752 (12:53445364 A>C,G,T), RS1001094261 (12:53444317 A>G), RS1001544409 (12:53440184 T>C), RS1001819118 (12:53446952 C>T), RS1002223040 (12:53444971 T>A), RS1002753090 (12:53441254 T>C), RS1002836063 (12:53442597 C>G), RS1003236204 (12:53441537 G>GC), RS1003323197 (12:53441589 G>A), RS1004829515 (12:53439786 A>T), RS1004902647 (12:53440504 C>A,G), RS1004933986 (12:53440819 C>T), RS1005002920 (12:53446561 T>C), RS1005118086 (12:53446137 G>A,C), RS1005542632 (12:53443421 A>G)

Disease associations

OMIM: gene MIM:610459 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004608_177	Granulocyte percentage of myeloid white cells	5.000000e-23
GCST004609_193	Monocyte percentage of white cells	1.000000e-22

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007997	granulocyte percentage of myeloid white cells
EFO:0007989	monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
methacrylaldehyde	affects cotreatment, decreases expression, increases oxidation, increases abundance	2
Acrolein	increases oxidation, increases abundance, affects cotreatment, decreases expression	2
Cisplatin	affects expression, affects cotreatment, increases expression	2
Ozone	affects cotreatment, decreases expression, increases oxidation, increases abundance	2
Valproic Acid	affects cotreatment, increases expression	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	decreases expression, increases oxidation, increases abundance, affects cotreatment	1
bisphenol A	affects expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	increases expression	1
aflatoxin B2	decreases methylation	1
S 1 (combination)	increases response to substance	1
jinfukang	increases expression, affects cotreatment	1
Irinotecan	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Decitabine	affects expression	1
Sunitinib	decreases expression	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance, increases oxidation	1
Cadmium	affects methylation	1
Fluorouracil	affects cotreatment, increases expression	1
Gallic Acid	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Lipopolysaccharides	affects expression, affects response to substance	1
Plant Extracts	affects cotreatment, decreases expression	1
Dronabinol	increases expression	1
Thiram	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Vitamin E	decreases expression	1

Clinical trials (associated diseases)

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