RPF1

Summary

RPF1 (ribosome production factor 1 homolog, HGNC:30350) is a protein-coding gene on chromosome 1p22.3, encoding Ribosome production factor 1 (Q9H9Y2). May be required for ribosome biogenesis. It is a common-essential gene (DepMap: required in 91.5% of cancer cell lines).

Enables RNA binding activity. Predicted to be involved in maturation of 5.8S rRNA and maturation of LSU-rRNA. Located in nucleolus.

Source: NCBI Gene 80135 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 81 total
• Cancer dependency (DepMap): dependent in 91.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_025065

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30350
Approved symbol	RPF1
Name	ribosome production factor 1 homolog
Location	1p22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000117133
Ensembl biotype	protein_coding
Entrez	80135

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000370654, ENST00000370656, ENST00000923273, ENST00000923274, ENST00000953136, ENST00000953137

RefSeq mRNA: 1 — MANE Select: NM_025065 NM_025065

CCDS: CCDS695

Canonical transcript exons

ENST00000370654 — 9 exons

Exon	Start	End
ENSE00000775626	84489633	84489728
ENSE00000830853	84482915	84482995
ENSE00001067179	84495373	84495455
ENSE00001067180	84496244	84496370
ENSE00001067182	84490319	84490472
ENSE00001067185	84495882	84496063
ENSE00001143789	84479266	84479509
ENSE00001162539	84480956	84481012
ENSE00001453239	84497429	84498352

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 96.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.2519 / max 842.0722, expressed in 1815 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
3798	43.2519	1815

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of sigmoid colon	UBERON:0004993	96.53	gold quality
palpebral conjunctiva	UBERON:0001812	96.51	gold quality
secondary oocyte	CL:0000655	96.08	gold quality
colonic mucosa	UBERON:0000317	95.62	gold quality
heart right ventricle	UBERON:0002080	95.46	gold quality
gluteal muscle	UBERON:0002000	95.44	gold quality
oral cavity	UBERON:0000167	95.42	gold quality
bronchial epithelial cell	CL:0002328	95.26	gold quality
deltoid	UBERON:0001476	95.23	gold quality
tibialis anterior	UBERON:0001385	94.94	gold quality
cartilage tissue	UBERON:0002418	94.89	gold quality
biceps brachii	UBERON:0001507	94.86	gold quality
skin of hip	UBERON:0001554	94.81	gold quality
triceps brachii	UBERON:0001509	94.76	gold quality
adult organism	UBERON:0007023	94.76	gold quality
corpus epididymis	UBERON:0004359	94.75	gold quality
parotid gland	UBERON:0001831	94.50	gold quality
myocardium	UBERON:0002349	94.50	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.49	gold quality
upper leg skin	UBERON:0004262	94.46	gold quality
epithelium of nasopharynx	UBERON:0001951	94.40	gold quality
epithelium of bronchus	UBERON:0002031	94.36	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	94.35	gold quality
superficial temporal artery	UBERON:0001614	94.26	gold quality
jejunal mucosa	UBERON:0000399	94.21	gold quality
bronchus	UBERON:0002185	94.09	gold quality
cauda epididymis	UBERON:0004360	94.01	gold quality
esophagus squamous epithelium	UBERON:0006920	93.92	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.75	gold quality
quadriceps femoris	UBERON:0001377	93.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

50 targeting RPF1, 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-548C-3P	99.99	74.01	7587
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-548BA	99.69	69.14	1514
HSA-MIR-548AI	99.69	69.24	1494
HSA-MIR-570-5P	99.69	69.24	1494
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-4687-3P	99.48	66.41	968

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 91.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

• Human RPF1 and ESF1 in Pre-rRNA Processing and the Assembly of Pre-Ribosomal Particles: A Functional Study. (PMID:38391939)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	rpf1	ENSDARG00000005738
mus_musculus	Rpf1	ENSMUSG00000028187
rattus_norvegicus	Rpf1	ENSRNOG00000015969
drosophila_melanogaster	CG6712	FBGN0032408
caenorhabditis_elegans		WBGENE00009711

Paralogs (1): IMP4 (ENSG00000136718)

Protein

Protein identifiers

Ribosome production factor 1 — Q9H9Y2 (reviewed: Q9H9Y2)

Alternative names: Brix domain-containing protein 5, Ribosome biogenesis protein RPF1

All UniProt accessions (2): Q9H9Y2, X6R7Q1

UniProt curated annotations — full annotation on UniProt →

Function. May be required for ribosome biogenesis.

Subcellular location. Nucleus. Nucleolus.

RefSeq proteins (1): NP_079341* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007109	Brix	Domain
IPR044281	IMP4/RPF1	Family

Pfam: PF04427

UniProt features (7 total): region of interest 2, sequence variant 2, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
8FKV	ELECTRON MICROSCOPY	2.47
8FKT	ELECTRON MICROSCOPY	2.81
8FKP	ELECTRON MICROSCOPY	2.85
8FKR	ELECTRON MICROSCOPY	2.89

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H9Y2-F1	86.01	0.72

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 103 (showing top): GOBP_RIBOSOME_BIOGENESIS, WANG_LMO4_TARGETS_DN, GOBP_MATURATION_OF_LSU_RRNA, GARY_CD5_TARGETS_DN, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, GOBP_MATURATION_OF_5_8S_RRNA, ACEVEDO_LIVER_CANCER_UP, chr1p22, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, GOCC_PRERIBOSOME, GOCC_PRERIBOSOME_LARGE_SUBUNIT_PRECURSOR, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX, SCGGAAGY_ELK1_02

GO Biological Process (4): maturation of 5.8S rRNA (GO:0000460), maturation of LSU-rRNA (GO:0000470), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (4): RNA binding (GO:0003723), rRNA primary transcript binding (GO:0042134), protein binding (GO:0005515), rRNA binding (GO:0019843)

GO Cellular Component (3): nucleolus (GO:0005730), preribosome, large subunit precursor (GO:0030687), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
rRNA processing	2
ribosomal large subunit biogenesis	1
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
ribonucleoprotein complex biogenesis	1
nucleic acid binding	1
rRNA binding	1
binding	1
RNA binding	1
nuclear lumen	1
intracellular membraneless organelle	1
preribosome	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1734 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RPF1	BRIX1	Q8TDN6	575
RPF1	RPF2	Q9H7B2	557
RPF1	NIFK	Q9BYG3	533
RPF1	NIP7	Q9Y221	479
RPF1	SBDS	Q9Y3A5	394
RPF1	WDR74	Q6RFH5	352
RPF1	WDR12	Q9GZL7	351
RPF1	BOP1	Q14137	350
RPF1	EBNA1BP2	Q99848	350
RPF1	TSR1	Q2NL82	349
RPF1	NOC2L	Q9Y3T9	349
RPF1	NSA2	O95478	349
RPF1	DCAF13	Q9NV06	348
RPF1	MAK16	Q9BXY0	348
RPF1	RRP15	Q9Y3B9	348

IntAct

127 interactions, top by confidence:

A	B	Type	Score
SART3	PRPF4	psi-mi:“MI:0914”(association)	0.730
KRTAP10-7	RPF1	psi-mi:“MI:0915”(physical association)	0.670
RPL14	RRP8	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
MECP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
NPM1	NVL	psi-mi:“MI:0914”(association)	0.610
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
RPL28	MAGEB2	psi-mi:“MI:0914”(association)	0.560
MAGEB10	GTPBP10	psi-mi:“MI:0914”(association)	0.530
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
RRP8	NVL	psi-mi:“MI:0914”(association)	0.530
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
MACROH2A2	PPM1G	psi-mi:“MI:0914”(association)	0.530
RPL18A	RRP8	psi-mi:“MI:0914”(association)	0.530
E4F1	ZBTB24	psi-mi:“MI:0914”(association)	0.530
ZCRB1	DKC1	psi-mi:“MI:0914”(association)	0.530
RPF1	ZNF324	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
MECP2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530

BioGRID (174): KRTAP10-7 (Two-hybrid), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS), KIAA0020 (Co-fractionation), RPF2 (Co-fractionation), RPL5 (Co-fractionation), RPF1 (Synthetic Lethality), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS), RPF1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D8PNQ6, G1TDB3, J9PAS6, O61749, O74172, P05749, P09132, P0C0T4, P0CX49, P0CX50, P14327, P34264, P37164, P37165, P48588, P49181, P52821, P56628, P62851, P62852, P62853, P79009, Q03409, Q09817, Q3E792, Q3ZBG7, Q4WX89, Q54VN6, Q54VZ4, Q56JX5, Q5B8Y4, Q5RBR1, Q6FPX5, Q6PBI5, Q6Q311, Q75DJ1, Q7SC06, Q8AVP1, Q8ISN9, Q8STD9

Diamond homologs: O13823, O14180, O62518, P53941, P54073, Q0VD01, Q5PQR5, Q5R631, Q5R947, Q5RJS9, Q6BYD9, Q6C804, Q6FNN7, Q6IQU6, Q755T8, Q7TND5, Q8AVP1, Q8VHZ7, Q96G21, Q9H9Y2, Q9VKB4, Q9YC08, P38805, Q975H1, Q5JDM5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 119 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
Peptide chain elongation	18	31.7×	7e-21
Viral mRNA Translation	18	31.7×	7e-21
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	18	31.4×	7e-21
Selenocysteine synthesis	18	30.1×	8e-21
Eukaryotic Translation Termination	18	30.1×	8e-21
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	18	29.4×	9e-21
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	18	29.4×	9e-21
Formation of a pool of free 40S subunits	18	28.0×	2e-20

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	18	31.1×	9e-20
ribosomal large subunit biogenesis	5	20.7×	2e-04
translation	19	18.2×	1e-16
ribosomal small subunit biogenesis	7	14.9×	5e-05
rRNA processing	10	13.2×	6e-07
regulation of alternative mRNA splicing, via spliceosome	5	11.4×	3e-03
nucleosome assembly	8	10.5×	7e-05
RNA processing	5	10.2×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

824 predictions. Top by Δscore:

Variant	Effect	Δscore
1:84479360:G:GT	donor_gain	1.0000
1:84479505:GGAAG:G	donor_gain	1.0000
1:84479506:GAAG:G	donor_gain	1.0000
1:84479506:GAAGG:G	donor_gain	1.0000
1:84479507:A:T	donor_gain	1.0000
1:84479508:AGGT:A	donor_loss	1.0000
1:84479509:GGT:G	donor_loss	1.0000
1:84479510:G:GA	donor_loss	1.0000
1:84479510:G:GG	donor_gain	1.0000
1:84480946:A:AG	acceptor_gain	1.0000
1:84480947:A:G	acceptor_gain	1.0000
1:84480948:C:G	acceptor_gain	1.0000
1:84480951:TTTAG:T	acceptor_loss	1.0000
1:84480952:TTAGG:T	acceptor_loss	1.0000
1:84480954:A:AG	acceptor_gain	1.0000
1:84480955:G:GG	acceptor_gain	1.0000
1:84480955:GGAAA:G	acceptor_gain	1.0000
1:84481008:ATAAG:A	donor_loss	1.0000
1:84481009:TAAGG:T	donor_loss	1.0000
1:84481010:AAG:A	donor_loss	1.0000
1:84481011:AGGTA:A	donor_loss	1.0000
1:84481012:GGTAA:G	donor_loss	1.0000
1:84481013:GTA:G	donor_loss	1.0000
1:84481014:T:A	donor_loss	1.0000
1:84482909:A:AG	acceptor_gain	1.0000
1:84482910:C:G	acceptor_gain	1.0000
1:84482910:CTTA:C	acceptor_loss	1.0000
1:84482913:A:AG	acceptor_gain	1.0000
1:84482913:AG:A	acceptor_gain	1.0000
1:84482913:AGGC:A	acceptor_loss	1.0000

AlphaMissense

2308 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:84490380:G:C	R175T	1.000
1:84490381:A:C	R175S	1.000
1:84490381:A:T	R175S	1.000
1:84489700:T:C	L145P	0.999
1:84489706:C:A	T147K	0.999
1:84489706:C:G	T147R	0.999
1:84490344:T:C	L163P	0.999
1:84490380:G:T	R175I	0.999
1:84490417:C:G	C187W	0.999
1:84490440:T:C	L195P	0.999
1:84490446:T:A	V197D	0.999
1:84495411:G:C	A219P	0.999
1:84495412:C:A	A219D	0.999
1:84495948:G:C	G256R	0.999
1:84495949:G:A	G256D	0.999
1:84495949:G:T	G256V	0.999
1:84495964:G:C	R261P	0.999
1:84496026:C:G	H282D	0.999
1:84496036:G:C	R285P	0.999
1:84496038:G:C	D286H	0.999
1:84496039:A:T	D286V	0.999
1:84496045:T:A	I288K	0.999
1:84496047:T:C	F289L	0.999
1:84496049:C:A	F289L	0.999
1:84496049:C:G	F289L	0.999
1:84496054:G:C	R291T	0.999
1:84496054:G:T	R291I	0.999
1:84496055:A:C	R291S	0.999
1:84496055:A:T	R291S	0.999
1:84496059:C:G	H293D	0.999

dbSNP variants (sampled 300 via entrez): RS1000046271 (1:84485183 C>A), RS1000510086 (1:84486625 G>A,T), RS1000831980 (1:84484874 A>G,T), RS1000873203 (1:84491871 C>T), RS1001191318 (1:84480782 A>C), RS1001318136 (1:84492883 T>C), RS1001387824 (1:84491305 T>C,G), RS1001402832 (1:84483610 A>G), RS1001596052 (1:84478086 A>G), RS1001603840 (1:84493291 A>T), RS1001717874 (1:84486494 A>C,T), RS1001735422 (1:84479757 C>G), RS1002048540 (1:84487989 A>G), RS1002429816 (1:84494239 G>A), RS1002483828 (1:84481243 A>G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	2
dicrotophos	decreases expression	1
deoxynivalenol	increases expression	1
aflatoxin B2	decreases methylation	1
cylindrospermopsin	increases expression	1
ICG 001	decreases expression	1
Temozolomide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Diethylstilbestrol	increases expression	1
Endosulfan	increases expression	1
Ozone	affects expression, increases abundance	1
Ribonucleotides	affects binding	1
Valproic Acid	affects expression	1
Aflatoxin B1	affects cotreatment, decreases expression	1
beta-Naphthoflavone	affects cotreatment, decreases expression	1
Copper Sulfate	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3G7	Abcam HEK293T RPF1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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