PRPF38B

Summary

PRPF38B (pre-mRNA processing factor 38B, HGNC:25512) is a protein-coding gene on chromosome 1p13.3, encoding Pre-mRNA-splicing factor 38B (Q5VTL8). May be required for pre-mRNA splicing. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of precatalytic spliceosome.

Source: NCBI Gene 55119 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 71 total
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_018061

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25512
Approved symbol	PRPF38B
Name	pre-mRNA processing factor 38B
Location	1p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10330, NET1
Ensembl gene	ENSG00000134186
Ensembl biotype	protein_coding
Entrez	55119

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000370021, ENST00000370022, ENST00000370025, ENST00000467302, ENST00000485810, ENST00000911741

RefSeq mRNA: 15 — MANE Select: NM_018061 NM_001349757, NM_001349758, NM_001349759, NM_001349761, NM_001349762, NM_001349763, NM_001349764, NM_001349765, NM_001349766, NM_001349767, NM_001349768, NM_001349769, NM_001349770, NM_001349771, NM_018061

CCDS: CCDS788, CCDS86003

Canonical transcript exons

ENST00000370025 — 6 exons

Exon	Start	End
ENSE00000958076	108698604	108698827
ENSE00001224290	108696277	108696337
ENSE00001866104	108692310	108692867
ENSE00003579163	108695702	108695770
ENSE00003650558	108696043	108696194
ENSE00003850316	108699162	108702928

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 96.70.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 90.4783 / max 8086.8488, expressed in 1824 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4353	62.6710	1823
4359	13.6397	1518
4354	3.9326	1419
4360	3.7071	1133
4361	2.2535	819
4357	1.2085	591
201603	0.9390	419
4358	0.8269	380
4362	0.6025	245
4363	0.5838	208

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
trabecular bone tissue	UBERON:0002483	96.70	gold quality
cerebellar hemisphere	UBERON:0002245	96.50	gold quality
cerebellar cortex	UBERON:0002129	96.40	gold quality
sural nerve	UBERON:0015488	96.39	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.32	gold quality
cerebellum	UBERON:0002037	95.86	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.73	gold quality
lymph node	UBERON:0000029	95.70	gold quality
body of pancreas	UBERON:0001150	95.70	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.59	gold quality
epithelium of nasopharynx	UBERON:0001951	95.46	gold quality
rectum	UBERON:0001052	95.37	gold quality
monocyte	CL:0000576	95.29	gold quality
mononuclear cell	CL:0000842	95.13	gold quality
spleen	UBERON:0002106	95.13	gold quality
caput epididymis	UBERON:0004358	95.02	gold quality
superficial temporal artery	UBERON:0001614	94.98	gold quality
corpus epididymis	UBERON:0004359	94.94	gold quality
leukocyte	CL:0000738	94.88	gold quality
metanephros cortex	UBERON:0010533	94.52	gold quality
right lung	UBERON:0002167	94.38	gold quality
transverse colon	UBERON:0001157	94.07	gold quality
minor salivary gland	UBERON:0001830	94.03	gold quality
small intestine	UBERON:0002108	93.87	gold quality
granulocyte	CL:0000094	93.79	gold quality
bone marrow	UBERON:0002371	93.75	gold quality
left lobe of thyroid gland	UBERON:0001120	93.61	gold quality
ventricular zone	UBERON:0003053	93.60	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.60	gold quality
cauda epididymis	UBERON:0004360	93.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-135	no	1227.61
E-CURD-89	no	850.80
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

158 targeting PRPF38B, 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-6873-3P	100.00	71.42	2626
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-5696	99.98	72.36	4487
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-12136	99.98	72.81	5713
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4482-3P	99.98	72.50	3147

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Pre-mRNA-splicing factor 38B — Q5VTL8 (reviewed: Q5VTL8)

Alternative names: Sarcoma antigen NY-SAR-27

All UniProt accessions (2): A0A0A0MRN0, Q5VTL8

UniProt curated annotations — full annotation on UniProt →

Function. May be required for pre-mRNA splicing.

Subcellular location. Nucleus.

Similarity. Belongs to the PRP38 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5VTL8-1	1	yes
Q5VTL8-2	2

RefSeq proteins (15): NP_001336686, NP_001336687, NP_001336688, NP_001336690, NP_001336691, NP_001336692, NP_001336693, NP_001336694, NP_001336695, NP_001336696, NP_001336697, NP_001336698, NP_001336699, NP_001336700, NP_060531* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005037	PRP38	Family

Pfam: PF03371

UniProt features (35 total): modified residue 14, compositionally biased region 12, region of interest 2, splice variant 2, sequence conflict 2, initiator methionine 1, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VTL8-F1	60.10	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 (14): 2, 5, 227, 288, 290, 318, 320, 448, 473, 475, 481, 527, 529, 534

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 521 (showing top): AP1_01, GOBP_RESPONSE_TO_IONIZING_RADIATION, JAEGER_METASTASIS_DN, CMYB_01, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_POSITIVE_REGULATION_OF_RHO_PROTEIN_SIGNAL_TRANSDUCTION, GOBP_GROWTH, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK, MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP, KYNG_DNA_DAMAGE_DN, KYNG_DNA_DAMAGE_BY_4NQO

GO Biological Process (3): mRNA processing (GO:0006397), RNA splicing (GO:0008380), mRNA splicing, via spliceosome (GO:0000398)

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (3): precatalytic spliceosome (GO:0071011), nucleus (GO:0005634), spliceosomal complex (GO:0005681)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
mRNA metabolic process	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
nucleic acid binding	1
spliceosomal complex	1
intracellular membrane-bounded organelle	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1

Protein interactions and networks

STRING

1391 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRPF38B	FAM89B	Q8N5H3	519
PRPF38B	SLC66A2	Q8N2U9	506
PRPF38B	EEIG2	Q5T8I3	452
PRPF38B	SCOC	Q9UIL1	452
PRPF38B	MED24	O75448	435
PRPF38B	H3BUI4	H3BUI4	432
PRPF38B	DLGAP3	O95886	424
PRPF38B	ATP6V1D	Q9Y5K8	423
PRPF38B	TEKT5	Q96M29	407
PRPF38B	RBM25	P49756	396
PRPF38B	FNDC7	Q5VTL7	369
PRPF38B	C19orf25	Q9UFG5	368
PRPF38B	RNPC3	Q96LT9	367
PRPF38B	ALDH18A1	P54886	349
PRPF38B	RIIAD1	A6NNX1	335

IntAct

81 interactions, top by confidence:

A	B	Type	Score
SUMO1	CBX4	psi-mi:“MI:0914”(association)	0.600
YWHAG	PRPF38B	psi-mi:“MI:0915”(physical association)	0.590
ZC3H18	AQR	psi-mi:“MI:0914”(association)	0.530
KIF2C	KIF2A	psi-mi:“MI:0914”(association)	0.530
SRPK2	RRP9	psi-mi:“MI:0914”(association)	0.530
EZH1	EPOP	psi-mi:“MI:0914”(association)	0.530
PRPF38B	NOP16	psi-mi:“MI:0915”(physical association)	0.400
PRPF38B	CYCS	psi-mi:“MI:0915”(physical association)	0.400
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
Bsdc1	SSB	psi-mi:“MI:0914”(association)	0.350
TBC1D9	SRSF2	psi-mi:“MI:0914”(association)	0.350
WRAP53	STK24	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CLK3	USP9Y	psi-mi:“MI:0914”(association)	0.350
JMJD6	U2SURP	psi-mi:“MI:0914”(association)	0.350
LUC7L	CASC3	psi-mi:“MI:0914”(association)	0.350
USP33	IFIT5	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
MAP1LC3A		psi-mi:“MI:0914”(association)	0.350
GABARAPL2		psi-mi:“MI:0914”(association)	0.350
GABARAPL1		psi-mi:“MI:0914”(association)	0.350
CEP170	FAM171A2	psi-mi:“MI:0914”(association)	0.350
ODF2	ELAPOR2	psi-mi:“MI:0914”(association)	0.350
JPH3	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
PTP4A3	POTEF	psi-mi:“MI:0914”(association)	0.350
TPX2	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350

BioGRID (128): PRPF38B (Affinity Capture-MS), PRPF38B (Co-fractionation), PRPF38B (Biochemical Activity), PRPF38B (Proximity Label-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS), PRPF38B (Affinity Capture-MS)

ESM2 similar proteins: A0A1S3XQD6, A0A1S4AX27, A1A5I1, A2AR02, A6QLS2, B0BN49, G2TRQ9, O14256, O55035, P30189, P30414, P41512, Q04750, Q07050, Q13427, Q27450, Q28EE8, Q3KPW4, Q4V9W2, Q505I5, Q59LQ5, Q5BKY9, Q5R8J6, Q5RJP9, Q5VTL8, Q5XHJ5, Q5ZLM8, Q6AXY7, Q6BNE1, Q6NQD9, Q6NWI1, Q6ZUT1, Q751P0, Q7L4I2, Q7YR26, Q80SY5, Q8GWY0, Q8N9E0, Q8N9Q2, Q8R0F5

Diamond homologs: Q5VTL8, Q6AXY7, Q6P7Y3, Q80SY5, Q8RWB1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 110 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
Transport of Mature Transcript to Cytoplasm	5	28.8×	6e-05
mRNA 3’-end processing	6	17.9×	7e-05
RNA Polymerase II Transcription Termination	5	16.6×	5e-04
mRNA Splicing	9	15.0×	2e-06
Transport of Mature mRNA derived from an Intron-Containing Transcript	6	13.8×	2e-04
Processing of Capped Intron-Containing Pre-mRNA	9	11.2×	1e-05
mRNA Splicing - Major Pathway	12	9.9×	9e-07
mRNA Polyadenylation	7	9.3×	5e-04

GO biological processes:

GO term	Partners	Fold	FDR
autophagosome maturation	5	18.5×	2e-03
regulation of alternative mRNA splicing, via spliceosome	5	12.8×	7e-03
RNA splicing	11	10.2×	6e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1034 predictions. Top by Δscore:

Variant	Effect	Δscore
1:108692867:GGTAC:G	donor_loss	1.0000
1:108692868:G:GG	donor_gain	1.0000
1:108692868:GT:G	donor_loss	1.0000
1:108695694:A:AG	acceptor_gain	1.0000
1:108695695:T:G	acceptor_gain	1.0000
1:108695697:TTCA:T	acceptor_loss	1.0000
1:108695698:TCAGG:T	acceptor_loss	1.0000
1:108695699:CAGGT:C	acceptor_loss	1.0000
1:108695700:A:AG	acceptor_gain	1.0000
1:108695700:AG:A	acceptor_gain	1.0000
1:108695701:G:GA	acceptor_gain	1.0000
1:108695701:GG:G	acceptor_gain	1.0000
1:108695701:GGT:G	acceptor_gain	1.0000
1:108695701:GGTC:G	acceptor_gain	1.0000
1:108695758:G:T	donor_gain	1.0000
1:108695766:GAGGG:G	donor_gain	1.0000
1:108695767:AGGG:A	donor_gain	1.0000
1:108695768:GGG:G	donor_gain	1.0000
1:108695768:GGGG:G	donor_gain	1.0000
1:108695769:GG:G	donor_gain	1.0000
1:108695769:GGG:G	donor_gain	1.0000
1:108695770:GG:G	donor_gain	1.0000
1:108695771:G:GG	donor_gain	1.0000
1:108695772:TAA:T	donor_loss	1.0000
1:108695781:G:GG	donor_gain	1.0000
1:108696025:AACTC:A	acceptor_gain	1.0000
1:108696026:ACTC:A	acceptor_gain	1.0000
1:108696029:C:A	acceptor_gain	1.0000
1:108696039:AAAG:A	acceptor_gain	1.0000
1:108696040:A:G	acceptor_gain	1.0000

AlphaMissense

3614 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:108692731:T:A	L47H	1.000
1:108692739:T:A	W50R	1.000
1:108692739:T:C	W50R	1.000
1:108692742:G:C	G51R	1.000
1:108692742:G:T	G51C	1.000
1:108692743:G:A	G51D	1.000
1:108692743:G:T	G51V	1.000
1:108692758:T:C	M56T	1.000
1:108692759:G:A	M56I	1.000
1:108692759:G:C	M56I	1.000
1:108692759:G:T	M56I	1.000
1:108692760:A:G	N57D	1.000
1:108692762:C:A	N57K	1.000
1:108692762:C:G	N57K	1.000
1:108692764:T:A	L58H	1.000
1:108692764:T:C	L58P	1.000
1:108692768:C:A	N59K	1.000
1:108692768:C:G	N59K	1.000
1:108692776:T:A	I62N	1.000
1:108692779:T:C	L63P	1.000
1:108692784:A:G	N65D	1.000
1:108692786:C:A	N65K	1.000
1:108692786:C:G	N65K	1.000
1:108692787:A:T	I66F	1.000
1:108692788:T:A	I66N	1.000
1:108692791:T:C	L67P	1.000
1:108692796:T:C	S69P	1.000
1:108692802:T:C	Y71H	1.000
1:108692802:T:G	Y71D	1.000
1:108692805:T:A	F72I	1.000

dbSNP variants (sampled 300 via entrez): RS1000130284 (1:108691792 T>C), RS1000397344 (1:108691507 GCTCT>G,GCT,GCTCTCT), RS1000406187 (1:108692224 G>A), RS1000458440 (1:108692355 C>A,G,T), RS1000824164 (1:108702075 A>G), RS1001169122 (1:108696806 G>A,T), RS1001401620 (1:108690856 A>T), RS1001462491 (1:108691164 A>C), RS1001703637 (1:108697094 A>G), RS1002066407 (1:108702491 G>A,T), RS1002102511 (1:108702296 G>T), RS1002304908 (1:108695606 A>C,G), RS1002577135 (1:108695240 G>A), RS1003228493 (1:108694407 A>G), RS1003262615 (1:108693915 T>C)

Disease associations

OMIM: gene `` | 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
GCST006444_22	Bone mineral density (hip)	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007702	hip bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	increases expression	2
bisphenol A	decreases expression, affects cotreatment	2
sodium arsenite	decreases expression, increases abundance, increases expression	2
Particulate Matter	decreases expression, increases abundance	2
FR900359	affects phosphorylation	1
deoxynivalenol	increases expression	1
zinc chromate	increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
coumarin	decreases phosphorylation	1
epigallocatechin gallate	increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
K 7174	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Hydrogen Peroxide	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Manganese	increases abundance, increases expression	1
Nicotine	increases expression	1
Phthalic Acids	decreases methylation	1

Clinical trials (associated diseases)

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