PRPF39

Summary

PRPF39 (pre-mRNA processing factor 39, HGNC:20314) is a protein-coding gene on chromosome 14q21.2, encoding Pre-mRNA-processing factor 39 (Q86UA1). Involved in pre-mRNA splicing. It is a selective cancer dependency (DepMap: 40.1% of cell lines).

Predicted to contribute to pre-mRNA 5’-splice site binding activity. Predicted to be involved in mRNA 5’-splice site recognition. Predicted to be located in nucleus. Predicted to be part of U1 snRNP; U2-type prespliceosome; and commitment complex.

Source: NCBI Gene 55015 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 75 total
• Cancer dependency (DepMap): dependent in 40.1% of screened cell lines
• MANE Select transcript: NM_017922

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20314
Approved symbol	PRPF39
Name	pre-mRNA processing factor 39
Location	14q21.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20666, FLJ11128
Ensembl gene	ENSG00000185246
Ensembl biotype	protein_coding
OMIM	614907
Entrez	55015

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 11 protein_coding, 5 nonsense_mediated_decay, 5 retained_intron

ENST00000355765, ENST00000424478, ENST00000477626, ENST00000553605, ENST00000554081, ENST00000554429, ENST00000554439, ENST00000554785, ENST00000556353, ENST00000556718, ENST00000556782, ENST00000557477, ENST00000905874, ENST00000905875, ENST00000905876, ENST00000931176, ENST00000931177, ENST00000931178, ENST00000961950, ENST00000961951, ENST00000961952

RefSeq mRNA: 1 — MANE Select: NM_017922 NM_017922

CCDS: CCDS9682

Canonical transcript exons

ENST00000355765 — 14 exons

Exon	Start	End
ENSE00002457523	45084116	45084249
ENSE00003469307	45114857	45116282
ENSE00003492952	45109616	45109780
ENSE00003497679	45112318	45112502
ENSE00003511541	45102529	45102696
ENSE00003524776	45110549	45110817
ENSE00003544691	45095221	45095563
ENSE00003582270	45114183	45114257
ENSE00003614513	45108415	45108522
ENSE00003631263	45110094	45110220
ENSE00003634464	45114494	45114614
ENSE00003636238	45096887	45097005
ENSE00003672369	45107451	45107616
ENSE00003786482	45096103	45096228

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 94.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.4166 / max 271.3708, expressed in 1801 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
139406	20.0657	1800
139408	2.1759	1049
139410	0.1145	33
139409	0.0604	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	94.82	gold quality
cerebellar cortex	UBERON:0002129	94.68	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.64	gold quality
body of pancreas	UBERON:0001150	93.81	gold quality
cerebellum	UBERON:0002037	93.22	gold quality
calcaneal tendon	UBERON:0003701	93.00	gold quality
skin of abdomen	UBERON:0001416	92.97	gold quality
left ovary	UBERON:0002119	92.86	gold quality
skin of leg	UBERON:0001511	92.54	gold quality
right ovary	UBERON:0002118	92.54	gold quality
adrenal tissue	UBERON:0018303	92.51	gold quality
mucosa of stomach	UBERON:0001199	92.45	gold quality
body of uterus	UBERON:0009853	92.25	gold quality
adenohypophysis	UBERON:0002196	91.92	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.81	gold quality
endocervix	UBERON:0000458	91.53	gold quality
muscle layer of sigmoid colon	UBERON:0035805	91.53	gold quality
tibial nerve	UBERON:0001323	91.32	gold quality
ventricular zone	UBERON:0003053	91.29	gold quality
metanephros cortex	UBERON:0010533	91.07	gold quality
right adrenal gland cortex	UBERON:0035827	91.01	gold quality
left adrenal gland cortex	UBERON:0035825	90.92	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	90.89	gold quality
ectocervix	UBERON:0012249	90.82	gold quality
left lobe of thyroid gland	UBERON:0001120	90.78	gold quality
ovary	UBERON:0000992	90.74	gold quality
minor salivary gland	UBERON:0001830	90.74	gold quality
left uterine tube	UBERON:0001303	90.68	gold quality
pituitary gland	UBERON:0000007	90.67	gold quality
zone of skin	UBERON:0000014	90.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

97 targeting PRPF39, 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-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 40.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

• Knockdown of PRPF39 expression resulted in a significant expression change of downstream gene. (PMID:22773733)
• organisms with higher splicing complexity have substituted the Prp39/Prp42 heterodimer with a PRPF39 homodimer (PMID:30949712)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	prpf39	ENSDARG00000100209
mus_musculus	Prpf39	ENSMUSG00000035597
rattus_norvegicus	Prpf39	ENSRNOG00000004521
drosophila_melanogaster	CG42272	FBGN0259167

Protein

Protein identifiers

Pre-mRNA-processing factor 39 — Q86UA1 (reviewed: Q86UA1)

Alternative names: PRP39 homolog

All UniProt accessions (5): Q86UA1, F8WB90, G3V5M7, H0YJR1, H0YJY9

UniProt curated annotations — full annotation on UniProt →

Function. Involved in pre-mRNA splicing.

Subcellular location. Nucleus.

Similarity. Belongs to the PRP39 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86UA1-1	1	yes
Q86UA1-2	2

RefSeq proteins (1): NP_060392* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003107	HAT	Repeat
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR059164	HAT_PRP39_C	Repeat

Pfam: PF23240, PF23241

UniProt features (18 total): repeat 7, compositionally biased region 4, splice variant 2, region of interest 2, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86UA1-F1	82.71	0.73

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 (1): 44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): MODULE_255, YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MODULE_317, CAGCTG_AP4_Q5, FREAC3_01, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, ATTCTTT_MIR186, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, GGCKCATGS_UNKNOWN, GOBP_MRNA_SPLICE_SITE_RECOGNITION, GOBP_MRNA_CIS_SPLICING_VIA_SPLICEOSOME

GO Biological Process (4): mRNA 5’-splice site recognition (GO:0000395), RNA processing (GO:0006396), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (2): protein binding (GO:0005515), pre-mRNA 5’-splice site binding (GO:0030627)

GO Cellular Component (4): commitment complex (GO:0000243), U1 snRNP (GO:0005685), U2-type prespliceosome (GO:0071004), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
U2-type spliceosomal complex	2
U1 snRNP	2
mRNA splice site recognition	1
mRNA cis splicing, via spliceosome	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
mRNA metabolic process	1
binding	1
pre-mRNA binding	1
spliceosomal snRNP complex	1
U2 snRNP	1
prespliceosome	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1716 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRPF39	LUC7L	Q9NQ29	622
PRPF39	PNISR	Q8TF01	589
PRPF39	LUC7L3	O95232	574
PRPF39	RBM25	P49756	560
PRPF39	SNRPC	P09234	543
PRPF39	A0A0A6YYJ8	A0A0A6YYJ8	534
PRPF39	LUC7L2	Q9Y383	530
PRPF39	SNRPA1	P09661	526
PRPF39	FKBP3	Q00688	521
PRPF39	PRP4K	Q13523	520
PRPF39	DDX46	Q7L014	481
PRPF39	PRPF18	Q99633	475
PRPF39	SNRNP70	P08621	472
PRPF39	P4HA1	P13674	458
PRPF39	EFTUD2	Q15029	457

IntAct

70 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
USE1	NBAS	psi-mi:“MI:0914”(association)	0.640
CFTR	HAX1	psi-mi:“MI:0914”(association)	0.610
PRPF39	TOLLIP	psi-mi:“MI:0915”(physical association)	0.560
CHAT	PRPF39	psi-mi:“MI:0915”(physical association)	0.560
PRPF39	ATN1	psi-mi:“MI:0915”(physical association)	0.560
PRPF39		psi-mi:“MI:0915”(physical association)	0.560
PRPF39	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
KLK6	PRPF39	psi-mi:“MI:0915”(physical association)	0.560
PRPF39	SMN1	psi-mi:“MI:0915”(physical association)	0.560
PRPF39		psi-mi:“MI:0915”(physical association)	0.550
EBNA-LP	HAX1	psi-mi:“MI:0914”(association)	0.530
PRPF39	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
TRNAU1AP	PRPF39	psi-mi:“MI:0915”(physical association)	0.400
FOXS1	DDX39A	psi-mi:“MI:0914”(association)	0.350

BioGRID (73): PRPF39 (Two-hybrid), PRPF39 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), KCTD15 (Affinity Capture-MS), ZNF318 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), PRPF39 (Reconstituted Complex), RNU1-1 (Protein-RNA), PRPF39 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), PRPF39 (Two-hybrid)

ESM2 similar proteins: A1A5S1, A1Z9G2, A7SK48, B3DJT0, B5X0I6, O36033, O42668, O74970, O76094, O94906, P0CO10, P0CO11, P19735, P33731, P41889, P87312, Q03560, Q12309, Q12381, Q13099, Q20255, Q23049, Q24314, Q2KJJ0, Q4KLU2, Q4PB37, Q4WVF4, Q527H0, Q52DF3, Q5B3U7, Q5BH69, Q5DM57, Q5RCC2, Q5RHH4, Q61371, Q6BSP7, Q6C186, Q6CAR6, Q6INC1, Q7SAK5

Diamond homologs: O74970, Q1JPZ7, Q4KLU2, Q86UA1, Q8K2Z2, Q93ZR3, B3DJT0, Q15020, Q5REG1, Q7KRW8, Q9JLI8, F4KHG8, Q6C186, P0CO10, P0CO11, P17886, P63154, P63155, P87312, Q12309, Q4PB37, Q4WT84, Q527H0, Q54XP4, Q5AED6, Q5BDX1, Q5K654, Q6BSP7, Q6CJK2, Q6FW76, Q750X3, Q7SGD2, Q9BZJ0, Q9HF03

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2925 predictions. Top by Δscore:

Variant	Effect	Δscore
14:45084246:TAAG:T	donor_loss	1.0000
14:45095459:G:GT	donor_gain	1.0000
14:45095519:GATTT:G	donor_gain	1.0000
14:45095529:GC:G	donor_gain	1.0000
14:45095530:C:G	donor_gain	1.0000
14:45095560:GGAG:G	donor_gain	1.0000
14:45095561:GAGG:G	donor_gain	1.0000
14:45096099:TCAG:T	acceptor_loss	1.0000
14:45096100:CAG:C	acceptor_loss	1.0000
14:45096101:A:AG	acceptor_gain	1.0000
14:45096101:AGAAT:A	acceptor_loss	1.0000
14:45096102:G:GG	acceptor_gain	1.0000
14:45096102:G:GT	acceptor_loss	1.0000
14:45096102:GA:G	acceptor_gain	1.0000
14:45096102:GAATC:G	acceptor_gain	1.0000
14:45096227:AG:A	donor_loss	1.0000
14:45096228:GGT:G	donor_loss	1.0000
14:45096229:G:GA	donor_loss	1.0000
14:45096230:T:G	donor_loss	1.0000
14:45097002:GAGG:G	donor_gain	1.0000
14:45097004:GG:G	donor_gain	1.0000
14:45097005:GG:G	donor_gain	1.0000
14:45107446:TTTA:T	acceptor_loss	1.0000
14:45107447:TTA:T	acceptor_loss	1.0000
14:45107448:TAG:T	acceptor_loss	1.0000
14:45107449:A:AG	acceptor_gain	1.0000
14:45107449:AG:A	acceptor_loss	1.0000
14:45107450:G:GG	acceptor_gain	1.0000
14:45107450:G:GT	acceptor_loss	1.0000
14:45107450:GA:G	acceptor_gain	1.0000

AlphaMissense

4484 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:45095522:T:C	F95L	1.000
14:45095524:T:A	F95L	1.000
14:45095524:T:G	F95L	1.000
14:45095531:T:A	W98R	1.000
14:45095531:T:C	W98R	1.000
14:45095544:T:C	L102P	1.000
14:45096160:T:C	C128R	1.000
14:45096161:G:A	C128Y	1.000
14:45096162:C:G	C128W	1.000
14:45096166:G:C	G130R	1.000
14:45096166:G:T	G130C	1.000
14:45096167:G:A	G130D	1.000
14:45096169:T:C	Y131H	1.000
14:45096172:T:A	W132R	1.000
14:45096172:T:C	W132R	1.000
14:45096174:G:C	W132C	1.000
14:45096174:G:T	W132C	1.000
14:45096178:A:G	K134E	1.000
14:45096184:G:C	A136P	1.000
14:45096185:C:A	A136E	1.000
14:45096899:G:A	G155R	1.000
14:45096899:G:C	G155R	1.000
14:45096899:G:T	G155W	1.000
14:45096900:G:A	G155E	1.000
14:45096920:A:C	S162R	1.000
14:45096922:T:A	S162R	1.000
14:45096922:T:G	S162R	1.000
14:45096930:T:C	L165P	1.000
14:45096932:T:A	W166R	1.000
14:45096932:T:C	W166R	1.000

dbSNP variants (sampled 300 via entrez): RS1000122019 (14:45096916 T>A), RS1000197738 (14:45089313 G>A), RS1000272675 (14:45116373 C>T), RS1000349328 (14:45101538 T>G), RS1000410212 (14:45097267 A>G), RS1000427663 (14:45108626 A>G), RS1000438325 (14:45115792 A>G), RS1000477384 (14:45094247 C>T), RS1000530472 (14:45115667 G>A), RS1000749449 (14:45115976 C>A), RS1000804674 (14:45087829 C>T), RS1000806081 (14:45108274 C>T), RS1000840862 (14:45084025 A>C,G), RS1001047369 (14:45088671 A>G), RS1001070162 (14:45088078 T>C)

Disease associations

OMIM: gene MIM:614907 | 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):

Study	Trait	p-value
GCST002935_20	Lead levels	7.000000e-06

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
Valproic Acid	affects expression, decreases expression, decreases methylation	5
sodium arsenite	increases abundance, increases expression, affects expression, decreases expression, affects cotreatment	3
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
dicrotophos	decreases expression	1
2,4,6-tribromophenol	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	decreases expression	1
trichostatin A	affects expression, decreases reaction	1
tris(2-butoxyethyl) phosphate	affects expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
jinfukang	decreases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Nickel	affects expression, decreases reaction	1
Ozone	increases oxidation, increases abundance, affects cotreatment	1
Phenobarbital	affects expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TH21	HAP1 PRPF39 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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