RRP36

Summary

RRP36 (ribosomal RNA processing 36, HGNC:21374) is a protein-coding gene on chromosome 6p21.1, encoding Ribosomal RNA processing protein 36 homolog (Q96EU6). Involved in the early processing steps of the pre-rRNA in the maturation pathway leading to the 18S rRNA. It is a selective cancer dependency (DepMap: 10.3% of cell lines).

RRP36 functions at an early stage in the processing of 35S preribosomal RNA into the mature 18S species (Gerus et al., 2010 [PubMed 20038530]).

Source: NCBI Gene 88745 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 61 total
• Cancer dependency (DepMap): dependent in 10.3% of screened cell lines
• MANE Select transcript: NM_033112

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21374
Approved symbol	RRP36
Name	ribosomal RNA processing 36
Location	6p21.1
Locus type	gene with protein product
Status	Approved
Aliases	dJ20C7.4
Ensembl gene	ENSG00000124541
Ensembl biotype	protein_coding
OMIM	613475
Entrez	88745

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000244496, ENST00000607394, ENST00000607555, ENST00000911397, ENST00000911398, ENST00000961657

RefSeq mRNA: 2 — MANE Select: NM_033112 NM_001329704, NM_033112

CCDS: CCDS34453

Canonical transcript exons

ENST00000244496 — 7 exons

Exon	Start	End
ENSE00000751529	43025263	43025329
ENSE00000751531	43026037	43026141
ENSE00000751532	43027178	43027252
ENSE00000751534	43027360	43027477
ENSE00000751536	43029092	43029599
ENSE00000974519	43021623	43021784
ENSE00000974520	43024985	43025132

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 95.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 112.0583 / max 707.6380, expressed in 1827 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
67852	108.3052	1827
67851	3.2571	1602
67853	0.4960	253

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	95.67	gold quality
islet of Langerhans	UBERON:0000006	94.65	gold quality
ileal mucosa	UBERON:0000331	94.63	gold quality
stromal cell of endometrium	CL:0002255	94.31	gold quality
calcaneal tendon	UBERON:0003701	93.92	gold quality
granulocyte	CL:0000094	93.79	gold quality
adenohypophysis	UBERON:0002196	93.55	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.29	gold quality
muscle of leg	UBERON:0001383	93.07	gold quality
gastrocnemius	UBERON:0001388	92.81	gold quality
mucosa of transverse colon	UBERON:0004991	92.78	gold quality
body of pancreas	UBERON:0001150	92.73	gold quality
right adrenal gland cortex	UBERON:0035827	92.71	gold quality
smooth muscle tissue	UBERON:0001135	92.53	gold quality
pancreas	UBERON:0001264	92.52	gold quality
left coronary artery	UBERON:0001626	92.49	gold quality
right adrenal gland	UBERON:0001233	92.44	gold quality
right coronary artery	UBERON:0001625	92.43	gold quality
ganglionic eminence	UBERON:0004023	92.35	gold quality
embryo	UBERON:0000922	92.34	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.33	gold quality
skin of leg	UBERON:0001511	92.31	gold quality
descending thoracic aorta	UBERON:0002345	92.26	gold quality
esophagus mucosa	UBERON:0002469	92.22	gold quality
thoracic aorta	UBERON:0001515	92.21	gold quality
left adrenal gland	UBERON:0001234	92.18	gold quality
ascending aorta	UBERON:0001496	92.18	gold quality
apex of heart	UBERON:0002098	92.12	gold quality
adrenal tissue	UBERON:0018303	92.04	gold quality
skin of abdomen	UBERON:0001416	91.97	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)

18 targeting RRP36, 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-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-3926	98.95	69.26	1438
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-4308	97.56	67.13	1385
HSA-MIR-4653-5P	97.22	67.72	1429
HSA-MIR-644A	96.02	66.52	786
HSA-MIR-1915-5P	95.25	65.78	571
HSA-MIR-887-3P	94.03	63.71	71

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 10.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• studied the orthologue of Rrp36p in HeLa cells, and showed that the function of this protein in early cleavages of the pre-rRNA has been conserved through evolution in eukaryotes (PMID:20038530)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	rrp36	ENSDARG00000032516
mus_musculus	Rrp36	ENSMUSG00000023971
rattus_norvegicus	Rrp36	ENSRNOG00000017836
drosophila_melanogaster	CG8461	FBGN0038235
caenorhabditis_elegans		WBGENE00020705

Protein

Protein identifiers

Ribosomal RNA processing protein 36 homolog — Q96EU6 (reviewed: Q96EU6)

All UniProt accessions (2): Q96EU6, U3KPZ9

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the early processing steps of the pre-rRNA in the maturation pathway leading to the 18S rRNA.

Subcellular location. Nucleus. Nucleolus.

Miscellaneous. Meningioma antigen.

Similarity. Belongs to the RRP36 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96EU6-1	1	yes
Q96EU6-2	2

RefSeq proteins (2): NP_001316633, NP_149103* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009292	RRP36	Family

Pfam: PF06102

UniProt features (10 total): region of interest 2, chain 1, coiled-coil region 1, short sequence motif 1, compositionally biased region 1, modified residue 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EU6-F1	83.06	0.50

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): 73

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72312	rRNA processing
R-HSA-8868773	rRNA processing in the nucleus and cytosol
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 83 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, HFH8_01, HAND1E47_01, ACEVEDO_LIVER_CANCER_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, AP4_01, REACTOME_METABOLISM_OF_RNA, GOCC_90S_PRERIBOSOME, GOCC_PRERIBOSOME, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX, SCGGAAGY_ELK1_02

GO Biological Process (4): maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462), rRNA processing (GO:0006364), ribosomal small subunit biogenesis (GO:0042274), ribosome biogenesis (GO:0042254)

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

GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), 90S preribosome (GO:0030686), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2
Metabolism of RNA	1
rRNA processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribosome biogenesis	2
ribonucleoprotein complex biogenesis	2
nuclear lumen	2
maturation of SSU-rRNA	1
RNA processing	1
rRNA metabolic process	1
nucleic acid binding	1
cellular anatomical structure	1
intracellular membraneless organelle	1
preribosome	1
t-UTP complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1404 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RRP36	UTP3	Q9NQZ2	768
RRP36	UTP20	O75691	716
RRP36	PDCD11	Q14690	689
RRP36	PRR35	P0CG20	648
RRP36	KBTBD12	Q3ZCT8	589
RRP36	RRP9	O43818	576
RRP36	HEATR1	Q9H583	552
RRP36	KRR1	Q13601	543
RRP36	SPMIP7	A4D263	538
RRP36	KLHDC8B	Q8IXV7	532
RRP36	KLC4	Q9NSK0	532
RRP36	BMS1	Q14692	527
RRP36	TOGARAM1	Q9Y4F4	527
RRP36	TRAPPC6B	Q86SZ2	522
RRP36	MAK16	Q9BXY0	520

IntAct

53 interactions, top by confidence:

A	B	Type	Score
GAR1	DKC1	psi-mi:“MI:0914”(association)	0.790
SUMO1	CBX4	psi-mi:“MI:0914”(association)	0.600
N	RBM47	psi-mi:“MI:0914”(association)	0.530
KIF2C	KIF2A	psi-mi:“MI:0914”(association)	0.530
EZH1	EPOP	psi-mi:“MI:0914”(association)	0.530
LINC00471	RRP36	psi-mi:“MI:0915”(physical association)	0.400
MAPT	MEX3A	psi-mi:“MI:0914”(association)	0.350
ORF4a	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
ARF5	SERPINH1	psi-mi:“MI:0914”(association)	0.350
LMNB1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
SRP19	RPS3A	psi-mi:“MI:0914”(association)	0.350
JPH3	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SAA1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
TPX2	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
COL8A1	CCDC85C	psi-mi:“MI:0914”(association)	0.350
ANOS1	ZNF724	psi-mi:“MI:0914”(association)	0.350
MALL	GPR89A	psi-mi:“MI:0914”(association)	0.350
LSM12	MCRIP1	psi-mi:“MI:0914”(association)	0.350
LINC02910	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
DNAJC22	UNC13B	psi-mi:“MI:0914”(association)	0.350
CXCL6	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
ANKRD50	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
GAGE5	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
ANAPC15	U2SURP	psi-mi:“MI:0914”(association)	0.350

BioGRID (76): RRP36 (Affinity Capture-MS), RRP12 (Co-fractionation), RRP36 (Affinity Capture-MS), RRP36 (Affinity Capture-MS), RRP36 (Affinity Capture-MS), RRP36 (Affinity Capture-MS), RRP36 (Affinity Capture-RNA), RRP36 (Proximity Label-MS), RRP36 (Synthetic Lethality), RRP36 (Affinity Capture-MS), RRP36 (Affinity Capture-MS), RRP36 (Proximity Label-MS), RRP36 (Proximity Label-MS), RRP36 (Affinity Capture-MS), RRP36 (Proximity Label-MS)

ESM2 similar proteins: A1A5P2, A6QNR1, A8WY26, D3ZND0, O15213, O59678, P27672, P78316, Q0V8M0, Q15050, Q24K12, Q28IV8, Q2KIH4, Q2KII6, Q3T0Q8, Q3T0Z5, Q3UFY0, Q4KLC4, Q5M985, Q5RAS1, Q5RJT2, Q5TAP6, Q5TJE7, Q5ZKM1, Q640M1, Q6EJB6, Q6P0I6, Q6PFJ1, Q8BK35, Q8IY81, Q8N9T8, Q8NEJ9, Q8R3N1, Q8VDQ9, Q96BZ8, Q96EU6, Q9BRP8, Q9BRR8, Q9BVJ6, Q9C086

Diamond homologs: A1CMA3, A1DLU6, A2R4K5, A3LP95, A4R1G4, A5DLD1, A5E0U1, A6QNR1, A6RF22, A6RKG5, A6ZPC2, A7E4K0, A7SL20, A7TMH4, A8Q6P6, B0CPQ8, B0YCZ3, B2B720, B2W2Y7, B3LJV1, B5VSG4, B6HGB5, B6K8A0, B6QVD3, B8MSM6, B8NDQ2, B9WMA4, C0NZV4, C0SGK2, C1GG27, C1GXI3, C4QVB0, C4Y4A0, C4YMC1, C5DF79, C5DPS9, C5FRS7, C5GLN0, C5JYW1, C5MAP5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

749 predictions. Top by Δscore:

Variant	Effect	Δscore
6:43021782:GGG:G	donor_gain	1.0000
6:43021783:GGG:G	donor_gain	1.0000
6:43024975:A:AG	acceptor_gain	1.0000
6:43024976:C:G	acceptor_gain	1.0000
6:43024979:CCACA:C	acceptor_loss	1.0000
6:43024980:CACAG:C	acceptor_loss	1.0000
6:43024981:ACAGG:A	acceptor_loss	1.0000
6:43024982:CAGGC:C	acceptor_loss	1.0000
6:43024983:A:AC	acceptor_loss	1.0000
6:43024983:A:AG	acceptor_gain	1.0000
6:43024984:G:GG	acceptor_gain	1.0000
6:43024984:GGCAC:G	acceptor_gain	1.0000
6:43026033:A:AG	acceptor_gain	1.0000
6:43026034:A:G	acceptor_gain	1.0000
6:43026036:GGTA:G	acceptor_gain	1.0000
6:43026139:G:GT	donor_gain	1.0000
6:43026139:GAG:G	donor_gain	1.0000
6:43026141:GGTAT:G	donor_loss	1.0000
6:43027169:A:AG	acceptor_gain	1.0000
6:43027169:AAT:A	acceptor_gain	1.0000
6:43027169:AATGT:A	acceptor_gain	1.0000
6:43027170:ATGT:A	acceptor_gain	1.0000
6:43027171:T:TA	acceptor_gain	1.0000
6:43027173:T:TA	acceptor_gain	1.0000
6:43027174:G:A	acceptor_gain	1.0000
6:43027358:A:AG	acceptor_gain	1.0000
6:43027358:AG:A	acceptor_gain	1.0000
6:43027359:G:GT	acceptor_gain	1.0000
6:43027359:GG:G	acceptor_gain	1.0000
6:43027359:GGA:G	acceptor_gain	1.0000

AlphaMissense

1676 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:43026109:T:C	F140L	0.997
6:43026111:C:A	F140L	0.997
6:43026111:C:G	F140L	0.997
6:43026055:T:C	F122L	0.996
6:43026057:T:A	F122L	0.996
6:43026057:T:G	F122L	0.996
6:43026052:C:A	R121S	0.989
6:43026091:T:C	F134L	0.989
6:43026093:T:A	F134L	0.989
6:43026093:T:G	F134L	0.989
6:43026110:T:C	F140S	0.987
6:43026047:A:G	D119G	0.984
6:43029174:G:C	K242N	0.984
6:43029174:G:T	K242N	0.984
6:43029124:T:C	F226L	0.983
6:43029126:C:A	F226L	0.983
6:43029126:C:G	F226L	0.983
6:43026048:C:A	D119E	0.982
6:43026048:C:G	D119E	0.982
6:43026056:T:C	F122S	0.978
6:43027465:T:C	F211L	0.977
6:43027467:C:A	F211L	0.977
6:43027467:C:G	F211L	0.977
6:43026052:C:G	R121G	0.976
6:43026113:T:C	L141S	0.975
6:43026110:T:G	F140C	0.974
6:43026103:T:G	Y138D	0.973
6:43026047:A:C	D119A	0.970
6:43026053:G:C	R121P	0.967
6:43029160:T:C	F238L	0.967

dbSNP variants (sampled 300 via entrez): RS1001475564 (6:43021236 C>T), RS1001623925 (6:43026646 C>T), RS1001819790 (6:43021489 T>C), RS1001918158 (6:43025408 G>C), RS1002242809 (6:43023611 G>C,T), RS1002368059 (6:43029206 A>G), RS1002399296 (6:43029495 T>C), RS1002870593 (6:43023261 T>G), RS1002910460 (6:43021225 C>T), RS1003039610 (6:43026184 G>C), RS1003065636 (6:43026441 G>C), RS1003540136 (6:43021087 C>G,T), RS1003758555 (6:43022396 C>A,G), RS1003920083 (6:43020006 T>C), RS1003933042 (6:43022734 G>A,C,T)

Disease associations

OMIM: gene MIM:613475 | 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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
sodium arsenite	increases expression, decreases expression	2
FR900359	decreases phosphorylation	1
methylmercuric chloride	decreases expression	1
bisphenol A	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Doxorubicin	increases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Lead	affects expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2EB	Abcam HeLa RRP36 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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