RPL36

gene
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Also known as DKFZp566B023L36eL36

Summary

RPL36 (ribosomal protein L36, HGNC:13631) is a protein-coding gene on chromosome 19p13.3, encoding RPL36 alternative reading frame protein (C0HME6). Inhibits C2CD2L/TMEM24-dependent transport of phosphatidylinositol, the precursor of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), from its site of synthesis in the endoplasmic reticulum to the cell membrane. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L36E family of ribosomal proteins. It is located in the cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome.

Source: NCBI Gene 25873 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 22 total
  • Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
  • MANE Select transcript: NM_033643

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13631
Approved symbolRPL36
Nameribosomal protein L36
Location19p13.3
Locus typegene with protein product
StatusApproved
AliasesDKFZp566B023, L36, eL36
Ensembl geneENSG00000130255
Ensembl biotypeprotein_coding
OMIM617893
Entrez25873

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 17 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000347512, ENST00000394580, ENST00000577222, ENST00000579446, ENST00000579649, ENST00000582380, ENST00000582463, ENST00000590786, ENST00000913550, ENST00000913551, ENST00000913552, ENST00000913553, ENST00000913554, ENST00000913555, ENST00000913556, ENST00000913557, ENST00000913558, ENST00000913559, ENST00000913560

RefSeq mRNA: 2 — MANE Select: NM_033643 NM_015414, NM_033643

CCDS: CCDS12147

Canonical transcript exons

ENST00000347512 — 4 exons

ExonStartEnd
ENSE0000115892456913195691453
ENSE0000271531856915325691875
ENSE0000272566256902955690327
ENSE0000274258356905065690600

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 99.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 442.8576 / max 2396.3547, expressed in 1827 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
173424299.97551827
173423139.97571824
1734153.38741178
1734252.90641287

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402399.80gold quality
cortical plateUBERON:000534399.78gold quality
left ovaryUBERON:000211999.77gold quality
ventricular zoneUBERON:000305399.77gold quality
embryoUBERON:000092299.74gold quality
ovaryUBERON:000099299.74gold quality
right ovaryUBERON:000211899.74gold quality
olfactory segment of nasal mucosaUBERON:000538699.73gold quality
left adrenal gland cortexUBERON:003582599.73gold quality
right adrenal glandUBERON:000123399.72gold quality
left adrenal glandUBERON:000123499.72gold quality
right uterine tubeUBERON:000130299.72gold quality
skin of abdomenUBERON:000141699.72gold quality
adrenal cortexUBERON:000123599.71gold quality
skin of legUBERON:000151199.71gold quality
penisUBERON:000098999.70gold quality
right adrenal gland cortexUBERON:003582799.70gold quality
endocervixUBERON:000045899.69gold quality
lower esophagus mucosaUBERON:003583499.69gold quality
granulocyteCL:000009499.68gold quality
nippleUBERON:000203099.68gold quality
adenohypophysisUBERON:000219699.68gold quality
body of pancreasUBERON:000115099.67gold quality
zone of skinUBERON:000001499.66gold quality
body of uterusUBERON:000985399.66gold quality
ectocervixUBERON:001224999.66gold quality
adrenal glandUBERON:000236999.65gold quality
gingival epitheliumUBERON:000194999.64gold quality
prostate glandUBERON:000236799.64gold quality
pituitary glandUBERON:000000799.63gold quality

Single-cell (SCXA)

Detected in 44 experiment(s), a significant marker in 10.

ExperimentMarker?Max mean expression
E-MTAB-9067yes6251.29
E-CURD-122yes97.72
E-CURD-88yes66.07
E-MTAB-9221yes57.37
E-CURD-112yes41.41
E-MTAB-10042yes14.52
E-HCAD-35yes9.40
E-MTAB-9801yes6.61
E-HCAD-31yes4.41
E-GEOD-125970no7118.15
E-MTAB-8410no6305.17
E-MTAB-6701no6226.33
E-CURD-85no5724.76
E-HCAD-4no5595.89
E-HCAD-24no5513.41

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 4)

  • RPL36 may be involved in the early stage of hepatocarcinogenesis, and it can be used as an independent and potential prognostic marker for resected hepatocellular carcinoma. (PMID:22029674)
  • These results provide evidence for a novel cell cycle regulatory network in glioma comprising the Long non-coding PLAC2 along with STAT1 and RPL36. (PMID:28922548)
  • Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24. (PMID:33479206)
  • The m6A reader IGF2BP1 attenuates the stability of RPL36 and cell proliferation to mediate benzene hematotoxicity by recognizing m6A modification. (PMID:38367942)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriorpl36ENSDARG00000100588
mus_musculusRpl36ENSMUSG00000057863
rattus_norvegicusRpl36l2ENSRNOG00000002340
rattus_norvegicusAABR07007675.1ENSRNOG00000029988
rattus_norvegicusRpl36l3ENSRNOG00000031947
rattus_norvegicusENSRNOG00000079694

Protein

Protein identifiers

RPL36 alternative reading frame proteinC0HME6 (reviewed: C0HME6, Q9Y3U8)

All UniProt accessions (3): Q9Y3U8, J3KTD3, J3QSB5

UniProt curated annotations — full annotation on UniProt →

Function. Inhibits C2CD2L/TMEM24-dependent transport of phosphatidylinositol, the precursor of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), from its site of synthesis in the endoplasmic reticulum to the cell membrane. This leads to down-regulation of the PI3K-AKT-mTOR signaling pathway.

Subunit / interactions. Interacts (when phosphorylated) with C2CD2L/TMEM24 (via the SMP-LBD and C2 domains); the interaction is required for localization of alt-RPL36 to the endoplasmic reticulum and inhibits C2CD2L-dependent transport of phosphatidylinositol from the endoplasmic reticulum to the cell membrane.

Subcellular location. Endoplasmic reticulum.

Post-translational modifications. Phosphorylation is regulated by cytosolic calcium levels. Increased calcium levels reduce phosphorylation at Ser-19, Ser-140 and Ser-142 but increase phosphorylation at Ser-22.

Miscellaneous. Produced by an alternative reading frame of the RPL36 gene which also produces ribosomal protein L36, a component of the large ribosomal subunit. Translation of alt-RPL36 initiates from a non-canonical GUG start codon upstream of the AUG start codon used to produce ribosomal protein L36.

RefSeq proteins (2): NP_056229, NP_378669* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000509Ribosomal_eL36Family
IPR038097Ribosomal_eL36_sfHomologous_superfamily

Pfam: PF01158

UniProt features (21 total): mutagenesis site 11, modified residue 5, chain 2, initiator methionine 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

194 structures, top 30 by resolution.

PDBMethodResolution (Å)
8A3DELECTRON MICROSCOPY1.67
8GLPELECTRON MICROSCOPY1.67
8QYXELECTRON MICROSCOPY1.78
8QOIELECTRON MICROSCOPY1.9
9O3WELECTRON MICROSCOPY1.9
8YOOELECTRON MICROSCOPY2
9C3HELECTRON MICROSCOPY2
9I2DELECTRON MICROSCOPY2.19
9PBEELECTRON MICROSCOPY2.19
8QFDELECTRON MICROSCOPY2.2
8YOPELECTRON MICROSCOPY2.2
9GULELECTRON MICROSCOPY2.2
9O3VELECTRON MICROSCOPY2.2
9O3YELECTRON MICROSCOPY2.2
8JDKELECTRON MICROSCOPY2.26
8G5YELECTRON MICROSCOPY2.29
9S3DELECTRON MICROSCOPY2.32
9RPVELECTRON MICROSCOPY2.35
9S3BELECTRON MICROSCOPY2.38
7OW7ELECTRON MICROSCOPY2.4
8K2CELECTRON MICROSCOPY2.4
8XSXELECTRON MICROSCOPY2.4
9SPFELECTRON MICROSCOPY2.4
9SPIELECTRON MICROSCOPY2.4
8JDLELECTRON MICROSCOPY2.42
9S3CELECTRON MICROSCOPY2.42
8FKVELECTRON MICROSCOPY2.47
9QLOELECTRON MICROSCOPY2.47
8FLEELECTRON MICROSCOPY2.48
9P8BELECTRON MICROSCOPY2.48

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y3U8-F193.200.88

No AlphaFold model available for C0HME6 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

C0HME6 (canonical)

Post-translational modifications (4): 19, 22, 140, 142

Mutagenesis-validated functional residues (11):

PositionPhenotype
98reduces alt-rpl36 protein levels. reduces phosphorylation. reduces interaction with c2cd2l.
104no effect on alt-rpl36 protein levels. reduces phosphorylation. reduces interaction with c2cd2l.
115reduces alt-rpl36 protein levels. reduces phosphorylation. reduces interaction with c2cd2l.
118no effect on alt-rpl36 protein levels. reduces phosphorylation. no effect on interaction with c2cd2l.
140reduces phosphorylation. abolishes phosphorylation and abolishes interaction with c2cd2l; when associated with a-19; a-2
142reduces phosphorylation. abolishes phosphorylation and abolishes interaction with c2cd2l; when associated with a-19; a-2
19reduces phosphorylation. abolishes phosphorylation and abolishes interaction with c2cd2l; when associated with a-22; a-1
22reduces phosphorylation. abolishes phosphorylation and abolishes interaction with c2cd2l; when associated with a-19; a-1
50reduces alt-rpl36 protein levels. reduces phosphorylation. abolishes interaction with c2cd2l.
73no effect on alt-rpl36 protein levels. no effect on phosphorylation. reduces interaction with c2cd2l.
93reduces alt-rpl36 protein levels. reduces phosphorylation. no effect on interaction with c2cd2l.

Q9Y3U8

Post-translational modifications (1): 62

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

IDPathway
R-HSA-156827L13a-mediated translational silencing of Ceruloplasmin expression
R-HSA-156902Peptide chain elongation
R-HSA-1799339SRP-dependent cotranslational protein targeting to membrane
R-HSA-192823Viral mRNA Translation
R-HSA-2408557Selenocysteine synthesis
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72689Formation of a pool of free 40S subunits
R-HSA-72706GTP hydrolysis and joining of the 60S ribosomal subunit
R-HSA-72764Eukaryotic Translation Termination
R-HSA-9010553Regulation of expression of SLITs and ROBOs
R-HSA-9633012Response of EIF2AK4 (GCN2) to amino acid deficiency
R-HSA-975956Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-975957Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-9954709Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide
R-HSA-9954714PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA
R-HSA-9954716ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA

MSigDB gene sets: 249 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, XU_GH1_AUTOCRINE_TARGETS_UP, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_MALE_GAMETE_GENERATION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_TRANSLATION, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_MUSCLE_CONTRACTION, GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN, GOBP_REGULATION_OF_SYNCYTIUM_FORMATION_BY_PLASMA_MEMBRANE_FUSION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GNF2_FBL, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_MYOTUBE_DIFFERENTIATION

GO Biological Process (2): cytoplasmic translation (GO:0002181), translation (GO:0006412)

GO Molecular Function (3): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), protein binding (GO:0005515)

GO Cellular Component (9): nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), cytosolic large ribosomal subunit (GO:0022625), cytosolic ribosome (GO:0022626), synapse (GO:0045202), ribosome (GO:0005840), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-11 pathways:

CategoryPathways
Ribosome-associated quality control3
Translation2
Cap-dependent Translation Initiation2
Nonsense-Mediated Decay (NMD)2
Eukaryotic Translation Initiation1
Eukaryotic Translation Elongation1
Influenza Viral RNA Transcription and Replication1
Selenoamino acid metabolism1
rRNA processing in the nucleus and cytosol1
Signaling by ROBO receptors1
Cellular response to starvation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
ribosome2
intracellular membraneless organelle2
translation1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
nucleic acid binding1
structural molecule activity1
binding1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
large ribosomal subunit1
cytosolic ribosome1
cytosol1
cell junction1
protein-containing complex1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance10
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3141 predictions. Top by Δscore:

VariantEffectΔscore
19:5678646:TGC:Tacceptor_gain1.0000
19:5678649:C:CCacceptor_gain1.0000
19:5679584:ACCTG:Adonor_loss1.0000
19:5679621:A:ACdonor_gain1.0000
19:5679622:C:CCdonor_gain1.0000
19:5679622:CTGG:Cdonor_gain1.0000
19:5679651:C:CTdonor_gain1.0000
19:5679652:C:CTdonor_gain1.0000
19:5679759:GGAAC:Gacceptor_gain1.0000
19:5679760:GAAC:Gacceptor_gain1.0000
19:5679761:AAC:Aacceptor_gain1.0000
19:5679762:AC:Aacceptor_gain1.0000
19:5679763:CC:Cacceptor_gain1.0000
19:5679764:C:CCacceptor_gain1.0000
19:5679764:CTG:Cacceptor_loss1.0000
19:5679771:C:CTacceptor_gain1.0000
19:5680532:T:TAdonor_gain1.0000
19:5686523:GCTGG:Gdonor_gain1.0000
19:5686524:C:Gdonor_gain1.0000
19:5687500:CAG:Cacceptor_loss1.0000
19:5687501:A:AGacceptor_gain1.0000
19:5687502:G:Aacceptor_loss1.0000
19:5687502:G:GGacceptor_gain1.0000
19:5687502:GGCC:Gacceptor_gain1.0000
19:5687533:A:AGacceptor_gain1.0000
19:5687533:ACTC:Aacceptor_gain1.0000
19:5687536:C:Aacceptor_gain1.0000
19:5687664:GTCAG:Gdonor_gain1.0000
19:5687665:TCAGG:Tdonor_loss1.0000
19:5687666:CAGGT:Cdonor_loss1.0000

AlphaMissense

685 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:5691391:C:AR56S1.000
19:5691395:C:AA57D1.000
19:5691400:G:AE59K1.000
19:5691404:T:CL60S1.000
19:5691407:T:CL61P1.000
19:5691421:G:CD66H1.000
19:5691422:A:TD66V1.000
19:5691424:A:GK67E1.000
19:5691425:A:TK67I1.000
19:5691426:A:CK67N1.000
19:5691426:A:TK67N1.000
19:5691431:C:AA69D1.000
19:5691434:T:AL70H1.000
19:5691434:T:CL70P1.000
19:5691439:T:CF72L1.000
19:5691440:T:CF72S1.000
19:5691441:T:AF72L1.000
19:5691441:T:GF72L1.000
19:5691447:G:CK74N1.000
19:5691447:G:TK74N1.000
19:5691452:G:TR76M1.000
19:5691535:G:AG78R1.000
19:5691535:G:CG78R1.000
19:5691535:G:TG78W1.000
19:5691536:G:AG78E1.000
19:5691536:G:TG78V1.000
19:5691551:C:TA83V1.000
19:5691561:G:CK86N1.000
19:5691561:G:TK86N1.000
19:5691572:T:CL90P1.000

dbSNP variants (sampled 300 via entrez): RS1000418305 (19:5692305 T>A,C), RS1001159971 (19:5691638 C>T), RS1002071399 (19:5689016 T>C), RS1002103875 (19:5689343 C>A), RS1002413035 (19:5690868 C>G,T), RS1002730634 (19:5689746 C>T), RS1004405522 (19:5688586 G>A), RS1004806778 (19:5692333 A>C,G), RS1005893551 (19:5688413 C>T), RS1006273770 (19:5690915 G>A), RS1006568382 (19:5690742 G>A), RS1006641704 (19:5691001 G>A), RS1006759096 (19:5691123 G>A,C), RS1008299431 (19:5688913 T>C), RS1008767930 (19:5689200 T>C)

Disease associations

OMIM: gene MIM:617893 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): myoepithelial tumor (MONDO:0002380)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D009208MyoepitheliomaC04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, affects cotreatment, increases methylation, decreases expression, increases expression5
sodium arsenitedecreases expression, increases expression3
Smokedecreases expression, increases abundance2
Tobacco Smoke Pollutiondecreases expression, increases methylation2
Valproic Acidaffects cotreatment, increases expression, increases methylation2
Particulate Matterdecreases expression, increases expression2
aristolochic acid Idecreases expression1
quinonedecreases expression, decreases reaction, affects binding, increases reaction, decreases methylation (+1 more)1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, increases expression, decreases expression1
tris(2-butoxyethyl) phosphateincreases expression1
arseniteaffects binding, increases reaction1
methylparabendecreases expression1
epigallocatechin gallateincreases expression1
azoxystrobinincreases expression1
chloropicrindecreases expression1
perfluoro-n-nonanoic acidincreases expression1
deguelinincreases expression1
fenpyroximateincreases expression1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamideincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
pyrimidifenincreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
pyrachlostrobinincreases expression1
jinfukangincreases expression1
LDN 193189affects cotreatment, decreases expression1
picoxystrobinincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03600649PHASE1UNKNOWNClinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196PHASE1/PHASE2UNKNOWNA Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272PHASE1/PHASE2RECRUITINGNRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190PHASE1/PHASE2RECRUITINGAlpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420Not specifiedCOMPLETEDMalignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): myoepithelial tumor