RMP24

Summary

RMP24 (ribonuclease MRP subunit p24, HGNC:28802) is a protein-coding gene on chromosome 18q12.2, encoding Ribonuclease MRP protein subunit p24 (Q32NC0). Specific component of the MRP ribonucleoprotein endoribonuclease, Rnase/Mrp complex, a ribonucleoprotein complex involved in pre-rRNA processing. It is a selective cancer dependency (DepMap: 21.7% of cell lines).

At a glance

• Clinical variants (ClinVar): 5 total — 3 pathogenic
• Cancer dependency (DepMap): dependent in 21.7% of screened cell lines
• MANE Select transcript: NM_031446

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28802
Approved symbol	RMP24
Name	ribonuclease MRP subunit p24
Location	18q12.2
Locus type	gene with protein product
Status	Approved
Aliases	PNAS-131, PNAS-124, HsT3108
Ensembl gene	ENSG00000141428
Ensembl biotype	protein_coding
OMIM	621218
Entrez	83608

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000269194, ENST00000333234, ENST00000587719, ENST00000587873, ENST00000592875, ENST00000593210, ENST00000610527, ENST00000618334

RefSeq mRNA: 4 — MANE Select: NM_031446 NM_001201474, NM_001201475, NM_001201476, NM_031446

CCDS: CCDS11916, CCDS56064, CCDS74212

Canonical transcript exons

ENST00000592875 — 5 exons

Exon	Start	End
ENSE00001294474	35972885	35972907
ENSE00001536103	35978835	35979278
ENSE00002759364	35972679	35972805
ENSE00002944384	35977410	35977600
ENSE00003593878	35974896	35975095

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 94.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.7884 / max 137.3274, expressed in 1811 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
169947	23.7532	1808
169948	2.8404	1175
169949	0.1949	68

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.01	gold quality
tibialis anterior	UBERON:0001385	93.17	gold quality
deltoid	UBERON:0001476	92.68	gold quality
quadriceps femoris	UBERON:0001377	91.93	gold quality
vastus lateralis	UBERON:0001379	91.48	gold quality
upper arm skin	UBERON:0004263	91.35	gold quality
right testis	UBERON:0004534	91.04	gold quality
left testis	UBERON:0004533	90.98	gold quality
testis	UBERON:0000473	90.87	gold quality
gastrocnemius	UBERON:0001388	90.74	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	90.69	gold quality
monocyte	CL:0000576	90.67	gold quality
muscle of leg	UBERON:0001383	90.65	gold quality
calcaneal tendon	UBERON:0003701	90.51	gold quality
biceps brachii	UBERON:0001507	90.50	gold quality
hindlimb stylopod muscle	UBERON:0004252	90.43	gold quality
leukocyte	CL:0000738	90.41	gold quality
skeletal muscle tissue	UBERON:0001134	90.37	gold quality
body of pancreas	UBERON:0001150	90.27	gold quality
muscle tissue	UBERON:0002385	89.87	gold quality
epithelial cell of pancreas	CL:0000083	89.79	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	89.56	gold quality
bone marrow	UBERON:0002371	89.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.24	gold quality
granulocyte	CL:0000094	89.17	gold quality
ganglionic eminence	UBERON:0004023	88.95	gold quality
parotid gland	UBERON:0001831	88.78	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.75	gold quality
myocardium	UBERON:0002349	88.69	silver quality
nasal cavity epithelium	UBERON:0005384	88.55	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting RMP24, 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-3646	100.00	73.56	5283
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-12136	99.98	72.81	5713
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-190A-5P	99.54	71.45	933
HSA-MIR-190B-5P	99.54	71.40	925
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-5100	99.11	67.52	1098

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 21.7% of screened cell lines.

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-184p18.2	ENSDARG00000077407
mus_musculus	2700062C07Rik	ENSMUSG00000024273
rattus_norvegicus	C18h18orf21	ENSRNOG00000015546

Protein

Protein identifiers

Ribonuclease MRP protein subunit p24 — Q32NC0 (reviewed: Q32NC0)

Alternative names: HBV X-transactivated gene 13 protein, HBV XAg-transactivated protein 13, Ribonuclease MRP subunit p24, UPF0711 protein C18orf21

All UniProt accessions (4): A0A087X0E7, Q32NC0, K7EM84, L7N2F3

UniProt curated annotations — full annotation on UniProt →

Function. Specific component of the MRP ribonucleoprotein endoribonuclease, Rnase/Mrp complex, a ribonucleoprotein complex involved in pre-rRNA processing.

Subunit / interactions. Component of RNase MRP complex which consists of a catalytic RNA moiety and at least 12 protein subunits; POP1, POP4, POP5, POP7, RPP14, RPP25, POP4, RPP30, RPP38, RPP40, RMP24 and RMP64. Many of these protein subunits are shared with the RNase P complex; however, RMP24 and RMP64 are specific to the RNase MRP complex and are absent in the RNase P complex.

Subcellular location. Nucleus.

Similarity. Belongs to the RMP24 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q32NC0-1	1	yes
Q32NC0-2	2

RefSeq proteins (4): NP_001188403, NP_001188404, NP_001188405, NP_113634* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029779	Rmp24-like	Family

Pfam: PF15719

UniProt features (10 total): modified residue 3, compositionally biased region 2, chain 1, region of interest 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
9UH7	ELECTRON MICROSCOPY	2.84
9UH9	ELECTRON MICROSCOPY	3.47
9UHA	ELECTRON MICROSCOPY	3.93

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q32NC0-F1	74.94	0.42

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): 126, 130, 139

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): chr18q12, DODD_NASOPHARYNGEAL_CARCINOMA_UP, ACEVEDO_LIVER_CANCER_UP, GOCC_SNO_S_RNA_CONTAINING_RIBONUCLEOPROTEIN_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, SCGGAAGY_ELK1_02, COLDREN_GEFITINIB_RESISTANCE_UP, MEISSNER_NPC_HCP_WITH_H3K4ME2, GOCC_RIBONUCLEASE_MRP_COMPLEX, CCTNTMAGA_UNKNOWN, ALKBH3_TARGET_GENES, CBX5_TARGET_GENES, ELF2_TARGET_GENES, FOXE1_TARGET_GENES, NAB2_TARGET_GENES

GO Biological Process (1): RNA processing (GO:0006396)

GO Molecular Function (0):

GO Cellular Component (2): ribonuclease MRP complex (GO:0000172), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
sno(s)RNA-containing ribonucleoprotein complex	1
endoribonuclease complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

294 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RMP24	RPRD1A	Q96P16	662
RMP24	ELP2	Q6IA86	530
RMP24	CCDC178	Q5BJE1	507
RMP24	ZNF396	Q96N95	506
RMP24	GALNT1	Q10472	503
RMP24	RNF41	Q9H4P4	500
RMP24	MOCOS	Q96EN8	483
RMP24	ZNF397	Q8NF99	479
RMP24	PNMA6A	P0CW24	479
RMP24	GAREM1	Q9H706	448
RMP24	TTC39C	Q8N584	432
RMP24	ANKRD52	Q8NB46	416
RMP24	STK17B	O94768	409
RMP24	KLHL14	Q9P2G3	399
RMP24	DDX55	Q8NHQ9	397

IntAct

46 interactions, top by confidence:

A	B	Type	Score
RPP25	POP7	psi-mi:“MI:0914”(association)	0.810
C18orf21	POP7	psi-mi:“MI:0914”(association)	0.640
POP4	POP7	psi-mi:“MI:0914”(association)	0.640
MECP2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
POP4	NME2P1	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
POP7	RPP40	psi-mi:“MI:0914”(association)	0.530
RPP25L	RPP40	psi-mi:“MI:0914”(association)	0.530
C18orf21	RPP40	psi-mi:“MI:0914”(association)	0.530
POP4	RPP40	psi-mi:“MI:0914”(association)	0.530
C18orf21	HEATR1	psi-mi:“MI:0915”(physical association)	0.400
Cbx1		psi-mi:“MI:0914”(association)	0.350
HUWE1	NCOA4	psi-mi:“MI:0914”(association)	0.350
HNRNPU		psi-mi:“MI:0914”(association)	0.350
KIF18A	NCOR1	psi-mi:“MI:0914”(association)	0.350
BAX	BDP1	psi-mi:“MI:0914”(association)	0.350
FBXO31	CCNQ	psi-mi:“MI:0914”(association)	0.350
KIF22	PSEN2	psi-mi:“MI:0914”(association)	0.350
Ar	CUX1	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350

BioGRID (178): C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), RPP25 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), RPP30 (Affinity Capture-MS), RPP40 (Affinity Capture-MS), RPP14 (Affinity Capture-MS)

ESM2 similar proteins: A4D161, A6H7A8, E1BGQ2, O70524, O75391, P29084, P29540, P70445, Q14161, Q15650, Q28J59, Q2KJF9, Q2NL14, Q2VPL9, Q32LC9, Q32NC0, Q3ZK22, Q4V8D7, Q4VA36, Q5R595, Q5R802, Q5R9D9, Q5RFL7, Q5XI52, Q5ZJK1, Q66H91, Q6AY70, Q7TNE3, Q861R7, Q86UT8, Q8BND4, Q8BQR4, Q8BXK4, Q8C790, Q8IWR0, Q8K2I9, Q8NFZ0, Q8VDD9, Q8WWQ0, Q922H9

Diamond homologs: Q05B49, Q1LUS5, Q32NC0, Q4V7D8, Q5XFZ0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
C18orf21	“form complex”	“Ribonuclease MRP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 47 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
tRNA processing in the nucleus	6	38.1×	2e-06
rRNA processing in the nucleus and cytosol	5	25.9×	1e-04
rRNA processing	5	23.6×	1e-04
Major pathway of rRNA processing in the nucleolus and cytosol	6	11.9×	4e-04
Metabolism of RNA	6	8.1×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
rRNA processing	7	24.2×	3e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
154073	GRCh38/hg38 18q11.1-12.3(chr18:20941324-40360620)x3	Pathogenic
58779	GRCh38/hg38 18q12.1-12.2(chr18:35097761-39379288)x3	Pathogenic
625733	GRCh37/hg19 18q12.2(chr18:33554981-36939357)	Pathogenic

SpliceAI

741 predictions. Top by Δscore:

Variant	Effect	Δscore
18:35972806:G:GG	donor_gain	1.0000
18:35975064:TGAAA:T	donor_gain	1.0000
18:35977403:AT:A	acceptor_gain	1.0000
18:35977404:T:TA	acceptor_gain	1.0000
18:35977407:TA:T	acceptor_loss	1.0000
18:35977408:A:AG	acceptor_gain	1.0000
18:35977408:AGTT:A	acceptor_gain	1.0000
18:35977409:G:GT	acceptor_gain	1.0000
18:35977409:GT:G	acceptor_gain	1.0000
18:35977409:GTT:G	acceptor_gain	1.0000
18:35977409:GTTG:G	acceptor_gain	1.0000
18:35977409:GTTGA:G	acceptor_gain	1.0000
18:35978829:TTTCA:T	acceptor_loss	1.0000
18:35978830:TTCAG:T	acceptor_loss	1.0000
18:35978831:TCA:T	acceptor_loss	1.0000
18:35978833:A:AG	acceptor_gain	1.0000
18:35978833:AG:A	acceptor_loss	1.0000
18:35978834:G:GG	acceptor_gain	1.0000
18:35978834:GA:G	acceptor_gain	1.0000
18:35978834:GAA:G	acceptor_gain	1.0000
18:35978834:GAAC:G	acceptor_gain	1.0000
18:35972906:CGGTA:C	donor_loss	0.9900
18:35972907:GGTAA:G	donor_loss	0.9900
18:35972908:GT:G	donor_loss	0.9900
18:35972909:T:A	donor_loss	0.9900
18:35974939:GCT:G	acceptor_gain	0.9900
18:35975065:GAAAA:G	donor_gain	0.9900
18:35975066:AAAAA:A	donor_gain	0.9900
18:35975093:TTGGT:T	donor_loss	0.9900
18:35975096:G:C	donor_loss	0.9900

AlphaMissense

1442 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:35972802:T:C	L25P	0.984
18:35974934:T:C	F47L	0.982
18:35974936:C:A	F47L	0.982
18:35974936:C:G	F47L	0.982
18:35974922:T:C	C43R	0.981
18:35974931:T:C	C46R	0.979
18:35974933:T:G	C46W	0.977
18:35974931:T:A	C46S	0.976
18:35974932:G:C	C46S	0.976
18:35977419:T:C	C104R	0.973
18:35972792:G:C	A22P	0.972
18:35974932:G:A	C46Y	0.972
18:35974968:G:C	R58P	0.969
18:35974981:A:C	K62N	0.968
18:35974981:A:T	K62N	0.968
18:35975087:A:C	S98R	0.968
18:35975089:T:A	S98R	0.968
18:35975089:T:G	S98R	0.968
18:35972805:T:C	L26P	0.965
18:35974924:T:G	C43W	0.965
18:35975072:T:C	F93L	0.965
18:35975074:C:A	F93L	0.965
18:35975074:C:G	F93L	0.965
18:35972759:G:C	A11P	0.963
18:35974967:C:A	R58S	0.963
18:35977428:T:A	C107S	0.961
18:35977429:G:C	C107S	0.961
18:35972780:T:C	C18R	0.960
18:35974923:G:A	C43Y	0.960
18:35974932:G:T	C46F	0.960

dbSNP variants (sampled 300 via entrez): RS1000292167 (18:35976370 C>T), RS1000738221 (18:35973643 A>G), RS1000980384 (18:35977660 G>A,C), RS1001521634 (18:35974866 G>A), RS1002286945 (18:35970876 C>T), RS1002527758 (18:35976422 A>G), RS1002727292 (18:35976736 C>T), RS1003526662 (18:35978051 T>A), RS1003676785 (18:35972115 C>T), RS1003759650 (18:35979389 C>T), RS1004207726 (18:35976843 T>C), RS1004218889 (18:35971842 G>C), RS1004304873 (18:35970923 C>A,T), RS1004546110 (18:35978204 T>C), RS1004606186 (18:35972207 C>G)

Disease associations

OMIM: gene MIM:621218 | 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)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2276314	C18orf21		0.00	0

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases abundance, increases expression	1
coumarin	increases phosphorylation	1
2-palmitoylglycerol	increases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	increases expression, increases abundance	1
Vehicle Emissions	increases abundance, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Sodium Dodecyl Sulfate	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	decreases expression	1
Cyclosporine	increases expression	1
Sodium Selenite	increases expression	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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