MRPS24

Summary

MRPS24 (mitochondrial ribosomal protein S24, HGNC:14510) is a protein-coding gene on chromosome 7p13, encoding Small ribosomal subunit protein uS3m (Q96EL2). It is a selective cancer dependency (DepMap: 44.7% of cell lines).

Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein. A pseudogene corresponding to this gene is found on chromosome 11. Read-through transcription exists between this gene and the upstream upregulator of cell proliferation (URGCP) gene.

Source: NCBI Gene 64951 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 25 total — 1 pathogenic
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 44.7% of screened cell lines
• MANE Select transcript: NM_032014

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14510
Approved symbol	MRPS24
Name	mitochondrial ribosomal protein S24
Location	7p13
Locus type	gene with protein product
Status	Approved
Aliases	MRP-S24, HSPC335
Ensembl gene	ENSG00000062582
Ensembl biotype	protein_coding
OMIM	611986
Entrez	64951

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000317534, ENST00000414932, ENST00000418740, ENST00000467084, ENST00000483330, ENST00000934254, ENST00000934255

RefSeq mRNA: 1 — MANE Select: NM_032014 NM_032014

CCDS: CCDS5473

Canonical transcript exons

ENST00000317534 — 4 exons

Exon	Start	End
ENSE00000832521	43869457	43869517
ENSE00003570906	43866558	43866982
ENSE00003644121	43868963	43869074
ENSE00003687563	43869308	43869376

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 90.2703 / max 352.0826, expressed in 1825 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
83815	88.3756	1823
83816	1.2936	469
83814	0.5513	282
83817	0.0498	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	98.76	gold quality
apex of heart	UBERON:0002098	98.67	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.67	gold quality
heart left ventricle	UBERON:0002084	98.40	gold quality
right adrenal gland	UBERON:0001233	98.31	gold quality
body of pancreas	UBERON:0001150	98.29	gold quality
muscle of leg	UBERON:0001383	98.26	gold quality
left adrenal gland	UBERON:0001234	98.25	gold quality
left adrenal gland cortex	UBERON:0035825	98.25	gold quality
right adrenal gland cortex	UBERON:0035827	98.22	gold quality
lower esophagus mucosa	UBERON:0035834	98.19	gold quality
right atrium auricular region	UBERON:0006631	98.15	gold quality
mucosa of transverse colon	UBERON:0004991	98.09	gold quality
heart	UBERON:0000948	98.00	gold quality
body of stomach	UBERON:0001161	97.94	gold quality
fundus of stomach	UBERON:0001160	97.90	gold quality
esophagus mucosa	UBERON:0002469	97.76	gold quality
adult mammalian kidney	UBERON:0000082	97.65	gold quality
right lobe of liver	UBERON:0001114	97.52	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.52	gold quality
skeletal muscle tissue	UBERON:0001134	97.49	gold quality
esophagus	UBERON:0001043	97.48	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.46	gold quality
prefrontal cortex	UBERON:0000451	97.43	gold quality
lower esophagus	UBERON:0013473	97.36	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.35	gold quality
cortex of kidney	UBERON:0001225	97.30	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.27	gold quality
saliva-secreting gland	UBERON:0001044	97.25	gold quality
minor salivary gland	UBERON:0001830	97.21	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	17.31
E-MTAB-10042	yes	14.33
E-MTAB-8894	no	134.09

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): YY1

miRNA regulators (miRDB)

13 targeting MRPS24, 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-3134	100.00	66.43	777
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4272	98.76	68.74	1810
HSA-MIR-493-3P	97.50	66.44	731
HSA-MIR-1910-5P	97.42	66.36	844
HSA-MIR-6826-5P	93.80	67.42	514
HSA-MIR-662	90.64	62.72	148

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 44.7% of screened cell lines.

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	mrps24	ENSDARG00000100116
mus_musculus	Mrps24	ENSMUSG00000020477
drosophila_melanogaster	mRpS24	FBGN0039159
caenorhabditis_elegans		WBGENE00023487

Protein

Protein identifiers

Small ribosomal subunit protein uS3m — Q96EL2 (reviewed: Q96EL2)

Alternative names: 28S ribosomal protein S24, mitochondrial, bMRP-47

All UniProt accessions (2): Q96EL2, F8VYR5

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Component of the mitochondrial small ribosomal subunit (mt-SSU). Mature mammalian 55S mitochondrial ribosomes consist of a small (28S) and a large (39S) subunit. The 28S small subunit contains a 12S ribosomal RNA (12S mt-rRNA) and 30 different proteins. The 39S large subunit contains a 16S rRNA (16S mt-rRNA), a copy of mitochondrial valine transfer RNA (mt-tRNA(Val)), which plays an integral structural role, and 52 different proteins.

Subcellular location. Mitochondrion.

Similarity. Belongs to the universal ribosomal protein uS3 family.

RefSeq proteins (1): NP_114403* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026146	Ribosomal_uS3m	Family

Pfam: PF14955

UniProt features (17 total): strand 7, helix 5, turn 2, transit peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

77 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
7QI4	ELECTRON MICROSCOPY	2.21
8CSS	ELECTRON MICROSCOPY	2.36
7P2E	ELECTRON MICROSCOPY	2.4
8RRI	ELECTRON MICROSCOPY	2.4
9OLF	ELECTRON MICROSCOPY	2.46
9OJM	ELECTRON MICROSCOPY	2.5
8CSQ	ELECTRON MICROSCOPY	2.54
8CSR	ELECTRON MICROSCOPY	2.54
6ZM6	ELECTRON MICROSCOPY	2.59
7QI5	ELECTRON MICROSCOPY	2.63
8CSP	ELECTRON MICROSCOPY	2.66
7PNX	ELECTRON MICROSCOPY	2.76
8ANY	ELECTRON MICROSCOPY	2.85
8CST	ELECTRON MICROSCOPY	2.85
6ZM5	ELECTRON MICROSCOPY	2.89
7PO0	ELECTRON MICROSCOPY	2.9
8K2A	ELECTRON MICROSCOPY	2.9
9PGL	ELECTRON MICROSCOPY	2.9
7PO1	ELECTRON MICROSCOPY	2.92
7PO3	ELECTRON MICROSCOPY	2.92
9PGF	ELECTRON MICROSCOPY	2.93
6VMI	ELECTRON MICROSCOPY	2.96
6RW4	ELECTRON MICROSCOPY	2.97
6VLZ	ELECTRON MICROSCOPY	2.97
7QI6	ELECTRON MICROSCOPY	2.98
8QRN	ELECTRON MICROSCOPY	2.98
9PSM	ELECTRON MICROSCOPY	2.98
8OIS	ELECTRON MICROSCOPY	3
9G5C	ELECTRON MICROSCOPY	3
9G5D	ELECTRON MICROSCOPY	3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EL2-F1	86.75	0.78

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-5368286	Mitochondrial translation initiation
R-HSA-5389840	Mitochondrial translation elongation
R-HSA-5419276	Mitochondrial translation termination
R-HSA-9937383	Mitochondrial ribosome-associated quality control
R-HSA-392499	Metabolism of proteins
R-HSA-5368287	Mitochondrial translation
R-HSA-72766	Translation

MSigDB gene sets: 116 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, MODULE_151, GOBP_MITOCHONDRIAL_TRANSLATION, GOBP_TRANSLATION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GOCC_MITOCHONDRIAL_ENVELOPE, chr7p13, ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN, MODULE_114, GOCC_RIBOSOME, GOCC_SMALL_RIBOSOMAL_SUBUNIT, GOCC_ORGANELLAR_RIBOSOME, GOCC_MITOCHONDRIAL_MATRIX, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_RIBOSOMAL_SUBUNIT

GO Biological Process (1): mitochondrial translation (GO:0032543)

GO Molecular Function (2): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial small ribosomal subunit (GO:0005763), ribosome (GO:0005840), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Mitochondrial translation	4
Translation	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mitochondrion	1
translation	1
mitochondrial gene expression	1
nucleic acid binding	1
structural molecule activity	1
ribosome	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
organellar small ribosomal subunit	1
mitochondrial ribosome	1
mitochondrial protein-containing complex	1
intracellular membraneless organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

149 interactions, top by confidence:

A	B	Type	Score
KBTBD7	METTL15	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
HSPD1	NUDT19	psi-mi:“MI:0914”(association)	0.710
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF331	USP9Y	psi-mi:“MI:0914”(association)	0.530
MRPS24	ZZEF1	psi-mi:“MI:0914”(association)	0.530
ZBTB48	ZBTB24	psi-mi:“MI:0914”(association)	0.530
E4F1	ZBTB24	psi-mi:“MI:0914”(association)	0.530
TRMT10B	MRPS14	psi-mi:“MI:0914”(association)	0.530
PDGFB	DKC1	psi-mi:“MI:0914”(association)	0.530
ZNF556	LRP4	psi-mi:“MI:0914”(association)	0.530
MRPS18B	MRPS14	psi-mi:“MI:0914”(association)	0.530
MRPL2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
ZNF707	ZNF316	psi-mi:“MI:0914”(association)	0.530
SNRNP70	GTPBP1	psi-mi:“MI:0914”(association)	0.530
CCDC59	GAPDHS	psi-mi:“MI:0914”(association)	0.530
MRPS34	ZZEF1	psi-mi:“MI:0914”(association)	0.530
MRPS18C	MRPS14	psi-mi:“MI:0914”(association)	0.530
ZFC3H1	HNRNPCL1	psi-mi:“MI:0914”(association)	0.530

BioGRID (342): MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MRPS24 (Affinity Capture-MS), MMADHC (Affinity Capture-MS), MRPS34 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS)

ESM2 similar proteins: A2A9C3, A2VD95, A4IG66, P0C2B8, P82649, Q01433, Q02356, Q0V9C9, Q1JPG0, Q2M2T7, Q3B8K3, Q3SX05, Q3SZV6, Q3ZBF3, Q499B3, Q4R5Q4, Q502C1, Q5BLE2, Q5EA71, Q5PQN9, Q5TC12, Q5U2X7, Q5XIC2, Q6NTS3, Q7L4E1, Q7Z7F7, Q810S1, Q811I0, Q861Y6, Q8BIW9, Q8BWM0, Q8K2M0, Q8VDR9, Q8WVB6, Q96DV4, Q96EL2, Q96HP0, Q9BQ95, Q9BSH3, Q9BUB7

Diamond homologs: Q2M2T7, Q3B8K3, Q502C1, Q61T16, Q688C0, Q6NTS3, Q96EL2, Q9CQV5, Q9VCC3

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
MRPS24	“form complex”	“28S mitochondrial small ribosomal subunit”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 161 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
Mitochondrial translation	21	27.5×	3e-23
Mitochondrial ribosome-associated quality control	23	26.9×	1e-24
Mitochondrial translation initiation	22	26.6×	7e-24
Mitochondrial translation elongation	22	26.6×	7e-24
Mitochondrial translation termination	22	23.0×	1e-22
Translation	25	14.8×	6e-21
Peptide chain elongation	7	8.5×	5e-04
Viral mRNA Translation	7	8.5×	5e-04

GO biological processes:

GO term	Partners	Fold	FDR
mitochondrial translation	24	28.2×	1e-25
RNA processing	10	14.8×	3e-07
translation	18	12.5×	2e-12
cytoplasmic translation	9	11.3×	2e-05
regulation of alternative mRNA splicing, via spliceosome	6	9.9×	3e-03
ribosomal small subunit biogenesis	6	9.2×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	24
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1047889	GRCh37/hg19 7p13-12.2(chr7:43341583-50171623)	Pathogenic

SpliceAI

314 predictions. Top by Δscore:

Variant	Effect	Δscore
7:43866979:TTAC:T	acceptor_gain	1.0000
7:43866980:TAC:T	acceptor_gain	1.0000
7:43866980:TACCT:T	acceptor_loss	1.0000
7:43866981:ACC:A	acceptor_loss	1.0000
7:43866982:CCT:C	acceptor_loss	1.0000
7:43866983:C:CC	acceptor_gain	1.0000
7:43868959:TCA:T	donor_loss	1.0000
7:43868960:CA:C	donor_loss	1.0000
7:43868960:CACCT:C	donor_loss	1.0000
7:43869070:CGGTT:C	acceptor_gain	1.0000
7:43869071:GGTT:G	acceptor_gain	1.0000
7:43869072:GTT:G	acceptor_gain	1.0000
7:43869072:GTTC:G	acceptor_loss	1.0000
7:43869073:TT:T	acceptor_gain	1.0000
7:43869074:TCTA:T	acceptor_loss	1.0000
7:43869075:C:CC	acceptor_gain	1.0000
7:43869075:CT:C	acceptor_loss	1.0000
7:43869075:CTA:C	acceptor_loss	1.0000
7:43869076:T:G	acceptor_loss	1.0000
7:43869305:CAC:C	donor_loss	1.0000
7:43869306:A:AC	donor_gain	1.0000
7:43869306:A:AT	donor_loss	1.0000
7:43869306:AC:A	donor_gain	1.0000
7:43869307:C:CC	donor_gain	1.0000
7:43869307:C:CT	donor_loss	1.0000
7:43869307:CC:C	donor_gain	1.0000
7:43866981:AC:A	acceptor_gain	0.9900
7:43866982:CC:C	acceptor_gain	0.9900
7:43868961:A:AC	donor_gain	0.9900
7:43868962:C:CC	donor_gain	0.9900

AlphaMissense

1057 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:43866786:A:C	S139R	0.993
7:43866786:A:T	S139R	0.993
7:43866788:T:G	S139R	0.993
7:43868985:T:A	K66N	0.993
7:43868985:T:G	K66N	0.993
7:43868986:T:A	K66I	0.991
7:43866903:G:C	F100L	0.988
7:43866903:G:T	F100L	0.988
7:43866905:A:G	F100L	0.988
7:43866870:C:A	K111N	0.987
7:43866870:C:G	K111N	0.987
7:43866938:C:G	D89H	0.986
7:43866760:T:A	K148I	0.985
7:43866918:G:C	F95L	0.985
7:43866918:G:T	F95L	0.985
7:43866920:A:G	F95L	0.985
7:43866904:A:G	F100S	0.983
7:43866919:A:G	F95S	0.982
7:43866869:G:T	R112S	0.979
7:43866931:A:G	F91S	0.977
7:43866801:G:C	F134L	0.975
7:43866801:G:T	F134L	0.975
7:43866803:A:G	F134L	0.975
7:43866930:G:C	F91L	0.975
7:43866930:G:T	F91L	0.975
7:43866932:A:G	F91L	0.975
7:43866708:C:A	K165N	0.973
7:43866708:C:G	K165N	0.973
7:43866791:A:C	Y138D	0.973
7:43868981:A:G	W68R	0.973

dbSNP variants (sampled 300 via entrez): RS1000104388 (7:43870222 G>A), RS1000269093 (7:43870798 C>T), RS1000342757 (7:43867557 T>A), RS1000808574 (7:43870501 T>C), RS1003533494 (7:43869177 C>T), RS1003658303 (7:43870864 C>T), RS1004530434 (7:43870960 A>G), RS1004729373 (7:43866350 C>A,G), RS1005634574 (7:43869771 TGA>T), RS1007189125 (7:43866172 G>A), RS1007564890 (7:43868313 C>T), RS1007885904 (7:43868026 C>T), RS1007946756 (7:43868633 G>A,C), RS1008117864 (7:43869459 G>A,T), RS1008479420 (7:43867047 G>C,T)

Disease associations

OMIM: gene MIM:611986 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001762_536	Obesity-related traits	7.000000e-06
GCST004487_8	Peak insulin response	4.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004887	maximal oxygen uptake measurement
EFO:0008000	peak insulin response measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067375 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.14	Kd	728.7	nM	CHEMBL5653589
6.09	ED50	811.7	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148778: Binding affinity to human MRPS24 incubated for 45 mins by Kinobead based pull down assay	kd	0.7287	uM

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects cotreatment, increases expression, affects expression	4
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
methylmercuric chloride	increases expression	1
bisphenol A	increases methylation	1
sulforaphane	decreases expression	1
coumarin	decreases phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
licochalcone B	increases expression	1
bisphenol S	increases methylation	1
Acetaminophen	decreases expression, affects cotreatment	1
Atrazine	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	increases expression	1
Hydralazine	increases expression, affects cotreatment	1
Ribonucleotides	affects binding	1
Sodium Selenite	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651820	Binding	Binding affinity to human MRPS24 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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