RSL24D1

gene
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Also known as HRP-L30-isoL30RPL24LRPL24

Summary

RSL24D1 (ribosomal L24 domain containing 1, HGNC:18479) is a protein-coding gene on chromosome 15q21.3, encoding Probable ribosome biogenesis protein RLP24 (Q9UHA3). Involved in the biogenesis of the 60S ribosomal subunit. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

This gene encodes a protein sharing a low level of sequence similarity with human ribosomal protein L24. Although this gene has been referred to as RPL24, L30, and 60S ribosomal protein L30 isolog in the sequence databases, it is distinct from the human genes officially named RPL24 (which itself has been referred to as ribosomal protein L30) and RPL30. The protein encoded by this gene localizes to the nucleolus and is thought to play a role in the biogenesis of the 60S ribosomal subunit. The precise function of this gene is currently unknown. This gene utilizes alternative polyadenylation signals and has multiple pseudogenes.

Source: NCBI Gene 51187 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 19 total
  • Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
  • MANE Select transcript: NM_016304

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18479
Approved symbolRSL24D1
Nameribosomal L24 domain containing 1
Location15q21.3
Locus typegene with protein product
StatusApproved
AliasesHRP-L30-iso, L30, RPL24L, RPL24
Ensembl geneENSG00000137876
Ensembl biotypeprotein_coding
OMIM613262
Entrez51187

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000260443, ENST00000562895, ENST00000562993, ENST00000564344, ENST00000565854, ENST00000569386, ENST00000677092, ENST00000677147, ENST00000677172, ENST00000677267, ENST00000677730, ENST00000677989, ENST00000932316

RefSeq mRNA: 1 — MANE Select: NM_016304 NM_016304

CCDS: CCDS10152

Canonical transcript exons

ENST00000260443 — 6 exons

ExonStartEnd
ENSE000008848225519681055196941
ENSE000011640255518080655182225
ENSE000035299115519272055192833
ENSE000035309495518331555183400
ENSE000036265935519097555191047
ENSE000036578805518536255185425

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 104.9187 / max 1506.8661, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
150066104.82851822
1500650.090226

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
germinal epithelium of ovaryUBERON:000130499.20gold quality
calcaneal tendonUBERON:000370198.76gold quality
parietal pleuraUBERON:000240098.67gold quality
cartilage tissueUBERON:000241898.66gold quality
cortical plateUBERON:000534398.64gold quality
tibiaUBERON:000097998.60gold quality
ganglionic eminenceUBERON:000402398.59gold quality
amniotic fluidUBERON:000017398.56gold quality
ventricular zoneUBERON:000305398.40gold quality
epithelium of nasopharynxUBERON:000195198.35gold quality
nasopharynxUBERON:000172898.33gold quality
pleuraUBERON:000097798.32gold quality
cauda epididymisUBERON:000436098.32gold quality
secondary oocyteCL:000065598.29gold quality
monocyteCL:000057698.19gold quality
mononuclear cellCL:000084298.15gold quality
embryoUBERON:000092298.15gold quality
superficial temporal arteryUBERON:000161498.07gold quality
caput epididymisUBERON:000435898.06gold quality
ovaryUBERON:000099298.05gold quality
left ovaryUBERON:000211998.03gold quality
leukocyteCL:000073898.02gold quality
penisUBERON:000098997.98gold quality
visceral pleuraUBERON:000240197.98gold quality
corpus epididymisUBERON:000435997.96gold quality
bone marrowUBERON:000237197.90gold quality
gingival epitheliumUBERON:000194997.84gold quality
islet of LangerhansUBERON:000000697.82gold quality
tendonUBERON:000004397.78gold quality
bone elementUBERON:000147497.77gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-10042yes5.53
E-MTAB-7606no402.51
E-MTAB-9689no340.78
E-GEOD-124858no231.22
E-HCAD-4no23.70
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting RSL24D1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4673100.0066.641490
HSA-MIR-3924100.0072.092394
HSA-MIR-5692A100.0074.406850
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-186-5P99.9970.833707
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-433-3P99.9869.371203
HSA-MIR-569699.9872.364487
HSA-MIR-60799.9773.625593
HSA-MIR-493-5P99.9672.472382
HSA-LET-7C-3P99.9573.422862
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-449599.8272.083080
HSA-MIR-808499.7369.571760
HSA-MIR-545-5P99.6670.182308
HSA-MIR-497-3P99.6169.711990
HSA-MIR-105-5P99.5469.242060
HSA-MIR-7853-5P99.5469.302055
HSA-MIR-519D-5P99.4169.302057
HSA-MIR-569599.4167.481047
HSA-MIR-569799.3967.741249
HSA-MIR-584-3P99.3567.691082
HSA-MIR-4777-5P99.3367.531148
HSA-MIR-128699.0966.231046
HSA-MIR-511-5P98.9770.942268
HSA-MIR-224-3P98.9168.421815

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 1)

  • RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. (PMID:36690642)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorsl24d1ENSDARG00000040439
mus_musculusRsl24d1ENSMUSG00000032215
rattus_norvegicusRsl24d1ENSRNOG00000052787
drosophila_melanogasterRpL24-likeFBGN0037899
caenorhabditis_elegansrpl-24.2WBGENE00004437

Paralogs (1): RPL24 (ENSG00000114391)

Protein

Protein identifiers

Probable ribosome biogenesis protein RLP24Q9UHA3 (reviewed: Q9UHA3)

Alternative names: Ribosomal L24 domain-containing protein 1, Ribosomal protein L24-like

All UniProt accessions (6): Q9UHA3, A0A7I2V2C6, A0A7I2V359, A0A7I2V3F2, H3BMQ2, H3BPF2

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of GTPBP4/NOG1 to pre-60S particles.

Subunit / interactions. Associated with nucleolar and cytoplasmic pre-60S particles. At the end of biogenesis it dissociates from cytoplasmic pre-60S particles and is likely to be exchanged for its ribosomal homolog, RPL24.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the eukaryotic ribosomal protein eL24 family.

RefSeq proteins (1): NP_057388* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000988Ribosomal_eL24-rel_NDomain
IPR011017TRASH_domDomain
IPR023442Ribosomal_eL24_CSConserved_site
IPR038630L24e/L24_sfHomologous_superfamily
IPR055345Ribosomal_eL24-like_arcFamily
IPR056366Ribosomal_eL24Family

Pfam: PF01246

UniProt features (6 total): sequence conflict 5, chain 1

Structure

Experimental structures (PDB)

39 structures, top 30 by resolution.

PDBMethodResolution (Å)
8FKVELECTRON MICROSCOPY2.47
8FLEELECTRON MICROSCOPY2.48
8FKWELECTRON MICROSCOPY2.5
8FL3ELECTRON MICROSCOPY2.53
8FL7ELECTRON MICROSCOPY2.55
8FLBELECTRON MICROSCOPY2.55
8FLDELECTRON MICROSCOPY2.58
8FKXELECTRON MICROSCOPY2.59
8FL6ELECTRON MICROSCOPY2.62
8FLAELECTRON MICROSCOPY2.63
8FLFELECTRON MICROSCOPY2.65
8FKYELECTRON MICROSCOPY2.67
8FL2ELECTRON MICROSCOPY2.67
8FL9ELECTRON MICROSCOPY2.75
8FKQELECTRON MICROSCOPY2.76
8FLCELECTRON MICROSCOPY2.76
8IDTELECTRON MICROSCOPY2.8
8FKTELECTRON MICROSCOPY2.81
8FKUELECTRON MICROSCOPY2.82
8RL2ELECTRON MICROSCOPY2.84
8FKPELECTRON MICROSCOPY2.85
8FKSELECTRON MICROSCOPY2.88
8FKRELECTRON MICROSCOPY2.89
8FL4ELECTRON MICROSCOPY2.89
8FL0ELECTRON MICROSCOPY2.91
8IDYELECTRON MICROSCOPY3
8INFELECTRON MICROSCOPY3
8FKZELECTRON MICROSCOPY3.04
9QIWELECTRON MICROSCOPY3.04
6LU8ELECTRON MICROSCOPY3.13

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UHA3-F191.630.80

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 418 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, GOBP_RIBOSOME_BIOGENESIS, MODULE_151, GOBP_RETINAL_GANGLION_CELL_AXON_GUIDANCE, MORF_UBE2I, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, HSIAO_HOUSEKEEPING_GENES, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_RIBOSOME_ASSEMBLY, GOBP_NEUROGENESIS, GOBP_MALE_GAMETE_GENERATION, GOBP_CRANIAL_NERVE_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_TRANSLATION

GO Biological Process (2): ribosomal large subunit biogenesis (GO:0042273), ribosome biogenesis (GO:0042254)

GO Molecular Function (2): structural constituent of ribosome (GO:0003735), protein binding (GO:0005515)

GO Cellular Component (3): nucleoplasm (GO:0005654), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ribonucleoprotein complex biogenesis2
nuclear lumen2
ribosome biogenesis1
structural molecule activity1
ribosome1
binding1
cellular anatomical structure1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

3001 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RSL24D1GTPBP4Q9BZE4941
RSL24D1NSA2O95478904
RSL24D1WDR12Q9GZL7865
RSL24D1MRTO4Q9UKD2848
RSL24D1GNL2Q13823843
RSL24D1NMD3Q96D46843
RSL24D1PAK1IP1Q9NWT1841
RSL24D1NIP7Q9Y221825
RSL24D1RPF2Q9H7B2810
RSL24D1NOP2P46087776
RSL24D1LSG1Q9H089775
RSL24D1WDR74Q6RFH5744
RSL24D1MDN1Q9NU22700
RSL24D1EBNA1BP2Q99848687
RSL24D1NOP53Q9NZM5665

IntAct

102 interactions, top by confidence:

ABTypeScore
RSL24D1DNMT3Lpsi-mi:“MI:0915”(physical association)0.780
DNMT3LRSL24D1psi-mi:“MI:0915”(physical association)0.780
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
RSL24D1FAM9Bpsi-mi:“MI:0915”(physical association)0.560
CDC23RSL24D1psi-mi:“MI:0915”(physical association)0.560
FAM9BRSL24D1psi-mi:“MI:0915”(physical association)0.560
RSL24D1CDC23psi-mi:“MI:0915”(physical association)0.560
RPL28MAGEB2psi-mi:“MI:0914”(association)0.560
FGF3GTPBP10psi-mi:“MI:0914”(association)0.530
MAGEB10GTPBP10psi-mi:“MI:0914”(association)0.530
RRP8NVLpsi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
MAK16NVLpsi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
PPANPPM1Gpsi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RSL24D1psi-mi:“MI:0915”(physical association)0.370
RSL24D1htpGpsi-mi:“MI:0915”(physical association)0.370
MKI67ARHGAP10psi-mi:“MI:0914”(association)0.350
CAND1GTPBP10psi-mi:“MI:0914”(association)0.350
CPNE4SUPT5Hpsi-mi:“MI:0914”(association)0.350
PPANIGF2BP3psi-mi:“MI:0914”(association)0.350

BioGRID (128): RSL24D1 (Two-hybrid), RSL24D1 (Two-hybrid), FAM9B (Two-hybrid), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS), RSL24D1 (Two-hybrid), RSL24D1 (Co-fractionation), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS), RSL24D1 (Affinity Capture-MS)

ESM2 similar proteins: A1XQU3, G1SE28, G1SKF7, G1SZ12, O65743, O70333, P37108, P38666, P40590, P46301, P50888, P50914, P61122, P83731, P83732, Q2YGT9, Q3SZ12, Q3T0U2, Q3ZC66, Q42347, Q4R5C7, Q5RBX7, Q5RF04, Q5SQF8, Q5ZKB6, Q63507, Q66WF5, Q6F444, Q6P6G7, Q6QMZ4, Q6Y263, Q792Q4, Q7SDU2, Q862I1, Q8BP67, Q8GYL5, Q8ISQ3, Q8JGR4, Q90YU3, Q962T5

Diamond homologs: A0B603, A1RXH7, A2BK96, A3DMR8, A4FYI7, A4YCQ3, A5UJN1, A6USH5, A6UT49, A6VJU5, A9A7E7, B6YWH7, C3MRJ8, C3MY94, C3MZM3, C3N7P5, C3NFS8, C4KIV3, C5A1V7, C6A1J2, G1SE28, O22165, O26357, O29492, P14116, P54064, P61122, P61123, P61124, P83731, P83732, Q07915, Q10353, Q12Z95, Q17606, Q3SZ12, Q4JAV2, Q5JGR5, Q5RF04, Q66WF5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 107 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:

PathwayPartnersFoldFDR
Peptide chain elongation2139.2×7e-27
Viral mRNA Translation2139.2×7e-27
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA2138.8×7e-27
Selenocysteine synthesis2137.1×1e-26
Eukaryotic Translation Termination2137.1×1e-26
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)2136.4×1e-26
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA2136.4×1e-26
Formation of a pool of free 40S subunits2134.6×4e-26

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation2139.7×6e-26
ribosomal large subunit biogenesis731.7×2e-07
translation2223.1×5e-22
ribosomal small subunit biogenesis818.6×7e-07
rRNA processing1014.4×2e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance14
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1004 predictions. Top by Δscore:

VariantEffectΔscore
15:55183312:CACCT:Cdonor_loss1.0000
15:55183313:A:ACdonor_gain1.0000
15:55183313:AC:Adonor_gain1.0000
15:55183313:ACCT:Adonor_loss1.0000
15:55183313:ACCTG:Adonor_gain1.0000
15:55183314:C:Adonor_loss1.0000
15:55183314:C:CAdonor_gain1.0000
15:55183314:CC:Cdonor_gain1.0000
15:55183314:CCT:Cdonor_gain1.0000
15:55183314:CCTG:Cdonor_gain1.0000
15:55183314:CCTGC:Cdonor_gain1.0000
15:55183396:TCAAT:Tacceptor_gain1.0000
15:55183397:CAAT:Cacceptor_gain1.0000
15:55183397:CAATC:Cacceptor_gain1.0000
15:55183398:AAT:Aacceptor_gain1.0000
15:55183398:AATCT:Aacceptor_gain1.0000
15:55183399:AT:Aacceptor_gain1.0000
15:55183399:ATCTA:Aacceptor_gain1.0000
15:55183400:TCTAC:Tacceptor_gain1.0000
15:55183401:C:CCacceptor_gain1.0000
15:55183401:CT:Cacceptor_gain1.0000
15:55183402:T:Aacceptor_gain1.0000
15:55183405:A:Tacceptor_gain1.0000
15:55183407:C:CTacceptor_gain1.0000
15:55183408:A:Tacceptor_gain1.0000
15:55183412:CATAT:Cacceptor_gain1.0000
15:55183413:A:Cacceptor_gain1.0000
15:55185356:TCATA:Tdonor_loss1.0000
15:55185357:CATAC:Cdonor_loss1.0000
15:55185358:ATAC:Adonor_loss1.0000

AlphaMissense

1103 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:55192764:A:GW51R1.000
15:55192764:A:TW51R1.000
15:55196824:G:TR23S1.000
15:55192750:G:CF55L0.999
15:55192750:G:TF55L0.999
15:55192752:A:GF55L0.999
15:55192760:G:AT52I0.999
15:55192762:C:AW51C0.999
15:55192762:C:GW51C0.999
15:55192778:G:TP46H0.999
15:55192780:A:CN45K0.999
15:55192780:A:TN45K0.999
15:55192795:A:CF40L0.999
15:55192795:A:TF40L0.999
15:55192797:A:GF40L0.999
15:55192807:A:CC36W0.999
15:55192808:C:TC36Y0.999
15:55192809:A:GC36R0.999
15:55192820:C:TC32Y0.999
15:55192821:A:GC32R0.999
15:55192822:A:CF31L0.999
15:55192822:A:TF31L0.999
15:55192823:A:GF31S0.999
15:55192824:A:GF31L0.999
15:55192828:G:CF29L0.999
15:55192828:G:TF29L0.999
15:55192830:A:GF29L0.999
15:55196816:A:CD25E0.999
15:55196816:A:TD25E0.999
15:55196817:T:AD25V0.999

dbSNP variants (sampled 300 via entrez): RS1000007114 (15:55194943 A>T), RS1000354723 (15:55189111 T>C), RS1000405235 (15:55191790 T>C), RS1000419426 (15:55186017 T>C), RS1000455958 (15:55185619 T>C), RS1000477500 (15:55181094 C>T), RS1000736175 (15:55193070 A>C,G), RS1000760403 (15:55187616 C>T), RS1001190004 (15:55192128 G>A,C), RS1001225223 (15:55194609 C>G,T), RS1001473808 (15:55197756 G>C,T), RS1001566534 (15:55180753 G>C), RS1001601982 (15:55183124 G>C), RS1001680598 (15:55186304 G>A), RS1001738055 (15:55197515 C>T)

Disease associations

OMIM: gene MIM:613262 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST001059_12Neutrophil count7.000000e-06
GCST003142_2Proteinuria in chronic kidney disease5.000000e-06
GCST005175_36Coronary artery calcified atherosclerotic plaque (90 or 130 HU threshold) in type 2 diabetes8.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004833neutrophil count
EFO:0004723coronary artery calcification

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression4
Valproic Acidaffects expression, decreases expression3
Air Pollutantsincreases abundance, increases expression, decreases expression2
Arsenicdecreases expression, increases abundance, increases expression2
Tretinoindecreases expression2
Cyclosporineincreases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
uranyl acetateaffects expression1
bisphenol Aaffects expression1
deoxynivalenolincreases expression1
beta-lapachoneincreases expression1
arseniteaffects binding, increases reaction1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
nivalenolincreases expression1
perfluorooctane sulfonic acidincreases expression1
chloropicrinaffects expression1
perfluoro-n-nonanoic acidincreases expression1
deguelinincreases expression1
fenpyroximateincreases expression1
pyrimidifenincreases expression1
torcetrapibincreases expression1
ICG 001increases expression1
thifluzamideincreases expression1
pyrachlostrobinincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
bisphenol Saffects cotreatment, increases expression1
jinfukangdecreases expression1
MT19c compoundincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.