RPL22L1

Summary

RPL22L1 (ribosomal protein L22 like 1, HGNC:27610) is a protein-coding gene on chromosome 3q26.2, encoding Ribosomal protein eL22-like (Q6P5R6). It is a selective cancer dependency (DepMap: 11.6% of cell lines).

Predicted to enable RNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in cytoplasmic translation. Predicted to be located in ribosome. Predicted to be part of ribonucleoprotein complex.

Source: NCBI Gene 200916 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 32 total
• Cancer dependency (DepMap): dependent in 11.6% of screened cell lines
• MANE Select transcript: NM_001099645

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27610
Approved symbol	RPL22L1
Name	ribosomal protein L22 like 1
Location	3q26.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000163584
Ensembl biotype	protein_coding
Entrez	200916

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000295830, ENST00000463836, ENST00000466674, ENST00000475836, ENST00000478578, ENST00000494771, ENST00000934973, ENST00000934974, ENST00000934975, ENST00000934976, ENST00000967081

RefSeq mRNA: 2 — MANE Select: NM_001099645 NM_001099645, NM_001320451

CCDS: CCDS46955, CCDS82875

Canonical transcript exons

ENST00000295830 — 4 exons

Exon	Start	End
ENSE00001076217	170868298	170868390
ENSE00001076218	170864875	170866524
ENSE00001076220	170868013	170868134
ENSE00001655874	170870159	170870195

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 98.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 94.6942 / max 1120.5912, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
45569	94.5483	1822
45568	0.1459	60

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cartilage tissue	UBERON:0002418	98.89	gold quality
lower esophagus mucosa	UBERON:0035834	98.23	gold quality
body of pancreas	UBERON:0001150	98.16	gold quality
upper arm skin	UBERON:0004263	97.90	gold quality
vermiform appendix	UBERON:0001154	97.78	gold quality
gingiva	UBERON:0001828	97.70	gold quality
gingival epithelium	UBERON:0001949	97.60	gold quality
ventricular zone	UBERON:0003053	97.48	gold quality
lymph node	UBERON:0000029	97.45	gold quality
pancreas	UBERON:0001264	97.34	gold quality
spleen	UBERON:0002106	97.27	gold quality
skin of abdomen	UBERON:0001416	97.19	gold quality
esophagus mucosa	UBERON:0002469	97.18	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.17	gold quality
bone marrow	UBERON:0002371	97.15	gold quality
islet of Langerhans	UBERON:0000006	97.03	gold quality
left ovary	UBERON:0002119	97.02	gold quality
oral cavity	UBERON:0000167	97.00	gold quality
monocyte	CL:0000576	96.95	gold quality
leukocyte	CL:0000738	96.77	gold quality
pericardium	UBERON:0002407	96.63	gold quality
mammalian vulva	UBERON:0000997	96.52	gold quality
bone marrow cell	CL:0002092	96.48	gold quality
right ovary	UBERON:0002118	96.40	gold quality
zone of skin	UBERON:0000014	96.26	gold quality
left uterine tube	UBERON:0001303	96.23	gold quality
omental fat pad	UBERON:0010414	96.22	gold quality
peritoneum	UBERON:0002358	96.21	gold quality
trabecular bone tissue	UBERON:0002483	96.05	gold quality
rectum	UBERON:0001052	95.85	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-MTAB-7407	yes	1110.89
E-CURD-98	yes	1077.62
E-HCAD-4	yes	142.26
E-HCAD-8	yes	47.70
E-HCAD-1	yes	45.44
E-CURD-112	yes	30.34
E-HCAD-9	yes	23.54
E-CURD-122	yes	22.24
E-MTAB-10042	yes	15.49
E-ANND-3	yes	14.44
E-MTAB-8271	yes	7.05
E-MTAB-6524	no	780.13
E-CURD-11	no	94.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting RPL22L1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
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-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-609	99.82	64.26	505
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-8084	99.73	69.57	1760

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 11.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

• RPL22L1 might be a prognostic marker in colorectal cancer and predict 5-Fluorouracil responsiveness. (PMID:31581233)
• Ribosomal protein L22-like1 promotes prostate cancer progression by activating PI3K/Akt/mTOR signalling pathway. (PMID:36625246)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	rpl22l1	ENSDARG00000010244
mus_musculus	Rpl22l1	ENSMUSG00000039221
rattus_norvegicus	Rpl22l3	ENSRNOG00000033819

Paralogs (1): RPL22 (ENSG00000116251)

Protein

Protein identifiers

Ribosomal protein eL22-like — Q6P5R6 (reviewed: Q6P5R6)

Alternative names: 60S ribosomal protein L22-like 1, Large ribosomal subunit protein eL22-like 1

All UniProt accessions (5): C9JYQ9, Q6P5R6, F8WDK8, H0Y8C2, Q5JWX6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the eukaryotic ribosomal protein eL22 family.

RefSeq proteins (2): NP_001093115, NP_001307380 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002671	Ribosomal_eL22	Family
IPR038526	Ribosomal_eL22_sf	Homologous_superfamily

Pfam: PF01776

UniProt features (5 total): modified residue 3, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P5R6-F1	88.63	0.78

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 (3): 112, 118, 120

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

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

MSigDB gene sets: 147 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, HORIUCHI_WTAP_TARGETS_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, KOINUMA_COLON_CANCER_MSI_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, chr3q26, GOBP_TRANSLATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, FISCHER_DREAM_TARGETS, VIETOR_IFRD1_TARGETS, REACTOME_METABOLISM_OF_RNA, GOCC_RIBOSOME, GOCC_RIBONUCLEOPROTEIN_COMPLEX, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP

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 (3): cytoplasm (GO:0005737), ribosome (GO:0005840), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-11 pathways:

Category	Pathways
Ribosome-associated quality control	3
Translation	2
Cap-dependent Translation Initiation	2
Nonsense-Mediated Decay (NMD)	2
Eukaryotic Translation Initiation	1
Eukaryotic Translation Elongation	1
Influenza Viral RNA Transcription and Replication	1
Selenoamino acid metabolism	1
rRNA processing in the nucleus and cytosol	1
Signaling by ROBO receptors	1
Cellular response to starvation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
translation	1
peptidyltransferase activity	1
translational initiation	1
translational elongation	1
translational termination	1
macromolecule biosynthetic process	1
protein metabolic process	1
protein biosynthetic process	1
nucleic acid binding	1
structural molecule activity	1
ribosome	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

2203 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RPL22L1	RPL38	P23411	691
RPL22L1	RPS14	P06366	687
RPL22L1	EIF5A2	Q9GZV4	633
RPL22L1	RPL9	P32969	632
RPL22L1	RPS27	P42677	618
RPL22L1	RPS27L	Q71UM5	617
RPL22L1	RPL3L	Q92901	575
RPL22L1	RPL10L	Q96L21	573
RPL22L1	RPS19	P39019	570
RPL22L1	RPL36AL	Q969Q0	566
RPL22L1	RPL39L	Q96EH5	565
RPL22L1	RPL5	P46777	560
RPL22L1	RPS9	P46781	535
RPL22L1	RPS24	P16632	527
RPL22L1	RPL11	P25121	527

IntAct

37 interactions, top by confidence:

A	B	Type	Score
RPL22L1	SDCBP2	psi-mi:“MI:0915”(physical association)	0.560
GRB2	ARHGEF35	psi-mi:“MI:0914”(association)	0.530
GIGYF2	RPL22L1	psi-mi:“MI:0915”(physical association)	0.400
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
BRD1	MRPS14	psi-mi:“MI:0914”(association)	0.350
KSR1	FBLL1	psi-mi:“MI:0914”(association)	0.350
KSR1	FAM168B	psi-mi:“MI:0914”(association)	0.350
KSR1		psi-mi:“MI:0914”(association)	0.350
MAD2L2		psi-mi:“MI:0914”(association)	0.350
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
COPS6	DDX3X	psi-mi:“MI:0914”(association)	0.350
RPL22L1	FAAP100	psi-mi:“MI:0914”(association)	0.350
USP39	RRP8	psi-mi:“MI:0914”(association)	0.350
G3BP2	FARS2	psi-mi:“MI:0914”(association)	0.350
MAP2K5	DNAJA2	psi-mi:“MI:0914”(association)	0.350
DUSP6	HSPA8	psi-mi:“MI:0914”(association)	0.350
PTPRR	TCP1	psi-mi:“MI:0914”(association)	0.350
LCK	CDK1	psi-mi:“MI:0914”(association)	0.350
FGFR1	POLRMT	psi-mi:“MI:0914”(association)	0.350
ARHGAP36	HAX1	psi-mi:“MI:0914”(association)	0.350
rep	TMEM120B	psi-mi:“MI:0914”(association)	0.350
CASP8	U2SURP	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
Npc1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CALM3	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
DNAJB1	HSPA8	psi-mi:“MI:0914”(association)	0.350
DRG1	RPS3A	psi-mi:“MI:0914”(association)	0.350
G3BP2	RPS3A	psi-mi:“MI:0914”(association)	0.350
ILF3	RPS3A	psi-mi:“MI:0914”(association)	0.350

BioGRID (1031): C17orf70 (Affinity Capture-MS), L3HYPDH (Affinity Capture-MS), VMAC (Affinity Capture-MS), MDM2 (Affinity Capture-MS), CCDC85B (Affinity Capture-MS), RPL22L1 (Affinity Capture-MS), RPL22L1 (Affinity Capture-RNA), RPL22L1 (Reconstituted Complex), RPL22L1 (Affinity Capture-MS), RPL22L1 (Affinity Capture-MS), VMAC (Affinity Capture-MS), C17orf70 (Affinity Capture-MS), CCDC85B (Affinity Capture-MS), L3HYPDH (Affinity Capture-MS), RPL22L1 (Affinity Capture-MS)

ESM2 similar proteins: A2YDY2, A4FUH0, G1TG89, G1TSG1, P35268, P42794, P42798, P47198, P48597, P50886, P50894, P52865, P62084, P62244, P62245, P62246, P62495, P62496, P62497, P62498, P67984, P67985, P86048, Q0DK10, Q0VCX5, Q28IL6, Q32L19, Q4R4D3, Q4R5I3, Q5I0R6, Q5NVP9, Q5R4C7, Q5R938, Q5U2Q7, Q6AYU1, Q6P5R6, Q6Q420, Q76I82, Q8BWY3, Q8CJ19

Diamond homologs: A0A1D8PM41, A4FUH0, G1TSG1, P05749, P13732, P35268, P47198, P50886, P50887, P52819, P52865, P56628, P67984, P67985, Q09668, Q23BV5, Q28IL6, Q4R5I3, Q54GK6, Q54JE3, Q5I0R6, Q6P5R6, Q90YU6, Q98TF8, Q9D7S7, Q9FE58, Q9M9W1, Q9SRX7, Q8SS49

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
RPL22	down-regulates	RPL22L1
RPL22L1	“form complex”	“60S cytosolic large ribosomal subunit”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 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
PKR-mediated signaling	6	21.7×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

261 predictions. Top by Δscore:

Variant	Effect	Δscore
3:170866520:AATAC:A	acceptor_gain	1.0000
3:170866521:ATAC:A	acceptor_gain	1.0000
3:170866522:TAC:T	acceptor_gain	1.0000
3:170866522:TACC:T	acceptor_loss	1.0000
3:170866524:CC:C	acceptor_loss	1.0000
3:170866524:CCT:C	acceptor_gain	1.0000
3:170866525:C:CC	acceptor_gain	1.0000
3:170866526:T:C	acceptor_gain	1.0000
3:170866526:T:TC	acceptor_gain	1.0000
3:170866527:T:C	acceptor_gain	1.0000
3:170866527:T:TC	acceptor_gain	1.0000
3:170866528:T:C	acceptor_gain	1.0000
3:170866528:T:TC	acceptor_gain	1.0000
3:170866533:A:AC	acceptor_gain	1.0000
3:170866533:A:C	acceptor_gain	1.0000
3:170868009:CAA:C	donor_loss	1.0000
3:170868009:CAACC:C	donor_gain	1.0000
3:170868010:AAC:A	donor_loss	1.0000
3:170868011:A:AC	donor_gain	1.0000
3:170868011:ACCT:A	donor_loss	1.0000
3:170868012:C:CC	donor_gain	1.0000
3:170868130:TGCTC:T	acceptor_gain	1.0000
3:170868132:CTC:C	acceptor_gain	1.0000
3:170868134:CCTA:C	acceptor_loss	1.0000
3:170868135:C:CC	acceptor_gain	1.0000
3:170868140:T:C	acceptor_gain	1.0000
3:170868140:T:TC	acceptor_gain	1.0000
3:170868292:ACTT:A	donor_loss	1.0000
3:170868294:TTA:T	donor_loss	1.0000
3:170868295:TACAA:T	donor_loss	1.0000

AlphaMissense

810 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:170866422:G:C	F109L	1.000
3:170866422:G:T	F109L	1.000
3:170866424:A:G	F109L	1.000
3:170866427:A:G	Y108H	1.000
3:170866468:A:G	L94P	1.000
3:170866468:A:T	L94H	1.000
3:170866470:C:A	W93C	1.000
3:170866470:C:G	W93C	1.000
3:170866472:A:G	W93R	1.000
3:170866472:A:T	W93R	1.000
3:170866495:A:G	L85P	1.000
3:170866495:A:T	L85H	1.000
3:170866503:C:A	K82N	1.000
3:170866503:C:G	K82N	1.000
3:170868015:T:A	K74N	1.000
3:170868015:T:G	K74N	1.000
3:170868324:C:G	D26H	1.000
3:170866423:A:G	F109S	0.999
3:170866426:T:C	Y108C	0.999
3:170866429:C:G	R107P	0.999
3:170866432:A:G	L106P	0.999
3:170866432:A:T	L106H	0.999
3:170866456:G:T	A98E	0.999
3:170866459:A:T	V97D	0.999
3:170866465:C:G	R95P	0.999
3:170866471:C:A	W93L	0.999
3:170866471:C:G	W93S	0.999
3:170866474:T:A	D92V	0.999
3:170866475:C:G	D92H	0.999
3:170866478:G:T	R91S	0.999

dbSNP variants (sampled 300 via entrez): RS1000162312 (3:170868912 G>A), RS1000306499 (3:170865766 C>T), RS1001383133 (3:170869777 C>T), RS1001981338 (3:170867025 T>C), RS1002305825 (3:170868366 A>G,T), RS1002500589 (3:170864643 A>C,T), RS1002768445 (3:170869383 T>C), RS1002802254 (3:170864941 G>A), RS1004263494 (3:170865280 C>T), RS1004631728 (3:170866912 A>G), RS1004740629 (3:170865428 TC>T), RS1005377995 (3:170869780 C>A,T), RS1005934490 (3:170866097 T>A,C), RS1006827383 (3:170870765 T>C), RS1006932843 (3:170870293 G>A,C,T)

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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, affects cotreatment	5
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression	5
sodium arsenite	decreases expression	4
Air Pollutants	increases abundance, increases expression, decreases expression, affects expression	4
trichostatin A	affects cotreatment, increases expression	3
entinostat	increases expression, affects cotreatment	2
Acetaminophen	decreases expression, increases expression	2
Benzo(a)pyrene	decreases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
deoxynivalenol	decreases expression	1
lead acetate	increases expression	1
tris(2-butoxyethyl) phosphate	increases expression	1
beta-lapachone	increases expression	1
arsenite	increases reaction, affects binding	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases expression, affects cotreatment	1
MT19c compound	increases expression	1
Cadmium	increases expression, increases abundance	1
Dexamethasone	affects cotreatment, decreases expression	1
Estradiol	decreases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1

Clinical trials (associated diseases)

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