RBM48

Summary

RBM48 (RNA binding motif protein 48, HGNC:21785) is a protein-coding gene on chromosome 7q21.2, encoding RNA-binding protein 48 (Q5RL73). As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs. It is a common-essential gene (DepMap: required in 91.7% of cancer cell lines).

Predicted to enable RNA binding activity. Predicted to be involved in RNA splicing and mRNA processing. Located in nucleoplasm.

Source: NCBI Gene 84060 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 87 total — 1 likely-pathogenic
• Phenotypes (HPO): 1
• Cancer dependency (DepMap): dependent in 91.7% of screened cell lines (common-essential)
• MANE Select transcript: NM_032120

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21785
Approved symbol	RBM48
Name	RNA binding motif protein 48
Location	7q21.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp564O0523, HSPC304
Ensembl gene	ENSG00000127993
Ensembl biotype	protein_coding
OMIM	621015
Entrez	84060

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000265732, ENST00000481551, ENST00000496410

RefSeq mRNA: 3 — MANE Select: NM_032120 NM_001363366, NM_001363367, NM_032120

CCDS: CCDS43615

Canonical transcript exons

ENST00000265732 — 5 exons

Exon	Start	End
ENSE00001280081	92532404	92532549
ENSE00001294734	92536851	92540481
ENSE00002462390	92534402	92534970
ENSE00003525278	92529476	92529666
ENSE00003841329	92528795	92528924

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 91.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.9474 / max 1485.4198, expressed in 1770 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
79528	15.9474	1770

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	91.40	gold quality
secondary oocyte	CL:0000655	90.88	gold quality
oocyte	CL:0000023	87.11	gold quality
medial globus pallidus	UBERON:0002477	86.02	gold quality
globus pallidus	UBERON:0001875	83.26	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.12	gold quality
tendon of biceps brachii	UBERON:0008188	82.63	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.52	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.47	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	80.49	gold quality
corpus callosum	UBERON:0002336	80.27	gold quality
right frontal lobe	UBERON:0002810	80.23	gold quality
bone marrow	UBERON:0002371	80.11	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	80.02	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	79.74	gold quality
gastrocnemius	UBERON:0001388	79.68	gold quality
muscle of leg	UBERON:0001383	79.45	gold quality
spinal cord	UBERON:0002240	79.45	gold quality
cerebellar hemisphere	UBERON:0002245	79.44	gold quality
cerebellar cortex	UBERON:0002129	79.43	gold quality
right hemisphere of cerebellum	UBERON:0014890	79.34	gold quality
monocyte	CL:0000576	79.27	gold quality
tendon	UBERON:0000043	79.26	gold quality
leukocyte	CL:0000738	79.21	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.17	gold quality
mononuclear cell	CL:0000842	79.00	gold quality
granulocyte	CL:0000094	78.90	gold quality
lower lobe of lung	UBERON:0008949	78.89	gold quality
cerebellum	UBERON:0002037	78.86	gold quality
jejunal mucosa	UBERON:0000399	78.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

104 targeting RBM48, 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-5692A	100.00	74.40	6850
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-3064-3P	100.00	70.09	1254
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-4282	99.99	75.36	6408
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 91.7% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

• Genetic analysis of human RNA binding motif protein 48 (RBM48) reveals an essential role in U12-type intron splicing. (PMID:36040194)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbm48	ENSDARG00000033754
mus_musculus	Rbm48	ENSMUSG00000040302
rattus_norvegicus	Rbm48	ENSRNOG00000008980
drosophila_melanogaster	CG34231	FBGN0085260

Protein

Protein identifiers

RNA-binding protein 48 — Q5RL73 (reviewed: Q5RL73)

All UniProt accessions (2): Q5RL73, C9J787

UniProt curated annotations — full annotation on UniProt →

Function. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs.

Subunit / interactions. Component of the minor spliceosome. Within this complex, interacts with ARMC7 and PRPF8/PRP8.

Similarity. Belongs to the RBM48 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5RL73-1	1	yes
Q5RL73-2	2

RefSeq proteins (3): NP_001350295, NP_001350296, NP_115496* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR034264	RBM48_RRM	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR039599	RBM48	Family

UniProt features (20 total): strand 5, helix 3, region of interest 3, sequence conflict 3, turn 2, chain 1, domain 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7DVQ	ELECTRON MICROSCOPY	2.89

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5RL73-F1	68.68	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, WTGAAAT_UNKNOWN, GOBP_RNA_SPLICING, CDPCR3HD_01, PARENT_MTOR_SIGNALING_UP, TGGAAA_NFAT_Q4_01, GOCC_CATALYTIC_STEP_2_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOCC_U12_TYPE_SPLICEOSOMAL_COMPLEX, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, GOBP_MRNA_PROCESSING, SHEN_SMARCA2_TARGETS_UP, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES

GO Biological Process (2): mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (3): RNA binding (GO:0003723), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (2): nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
mRNA metabolic process	1
nucleic acid binding	1
nuclear lumen	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1

Protein interactions and networks

STRING

1612 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM48	ARMC7	Q9H6L4	766
RBM48	FAM133B	Q5BKY9	540
RBM48	FAM186B	Q8IYM0	525
RBM48	THAP8	Q8NA92	507
RBM48	GATAD1	Q8WUU5	506
RBM48	ANKIB1	Q9P2G1	477
RBM48	HEPACAM2	A8MVW5	438
RBM48	ZNF483	Q8TF39	398
RBM48	SCNM1	Q9BWG6	394
RBM48	FAM168B	A1KXE4	371
RBM48	TMEM243	Q9BU79	370
RBM48	ZNF713	Q8N859	364
RBM48	VMA22	Q96NT0	358
RBM48	THOC3	Q96J01	354
RBM48	ALKBH6	Q3KRA9	347

IntAct

124 interactions, top by confidence:

A	B	Type	Score
RBM48	ARMC7	psi-mi:“MI:0915”(physical association)	0.800
TEKT4	RBM48	psi-mi:“MI:0915”(physical association)	0.560
S100Z	RBM48	psi-mi:“MI:0915”(physical association)	0.560
PIBF1	RBM48	psi-mi:“MI:0915”(physical association)	0.560
RBM48	EIF1AD	psi-mi:“MI:0915”(physical association)	0.560
RBM48	TSR2	psi-mi:“MI:0915”(physical association)	0.560
RBM48	KIF9	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	RBM48	psi-mi:“MI:0915”(physical association)	0.560
RBM48	ATPAF2	psi-mi:“MI:0915”(physical association)	0.560
MLH1	RBM48	psi-mi:“MI:0915”(physical association)	0.560
RAD51D	RBM48	psi-mi:“MI:0915”(physical association)	0.560
RBM48	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
RBM48	TBC1D22B	psi-mi:“MI:0915”(physical association)	0.560
RBM48	SPRED2	psi-mi:“MI:0915”(physical association)	0.560
COX5B	RBM48	psi-mi:“MI:0915”(physical association)	0.560
POLR1C	RBM48	psi-mi:“MI:0915”(physical association)	0.560
AMOT	RBM48	psi-mi:“MI:0915”(physical association)	0.560
PRKAB2	RBM48	psi-mi:“MI:0915”(physical association)	0.560
RBM48	FAM90A1	psi-mi:“MI:0915”(physical association)	0.560
GYS1	RBM48	psi-mi:“MI:0915”(physical association)	0.560
RBM48	JMY	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	RBM48	psi-mi:“MI:0915”(physical association)	0.560
RBM48	TEKT4	psi-mi:“MI:0915”(physical association)	0.560
RBM48	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
RBM48	S100Z	psi-mi:“MI:0915”(physical association)	0.560
NUDT21	RBM48	psi-mi:“MI:0915”(physical association)	0.550
TK1	RBM48	psi-mi:“MI:0915”(physical association)	0.550
RBM48	NBEA	psi-mi:“MI:0914”(association)	0.530

BioGRID (93): RBM48 (Affinity Capture-MS), ARMC7 (Affinity Capture-MS), ARMC7 (Affinity Capture-Western), RBM48 (Affinity Capture-Western), NBEA (Affinity Capture-MS), ARMC7 (Affinity Capture-MS), RBM48 (Two-hybrid), RBM48 (Two-hybrid), RBM48 (Two-hybrid), RBM48 (Two-hybrid), RBM48 (Two-hybrid), RBM48 (Two-hybrid), RBM48 (Two-hybrid), RBM48 (Two-hybrid), RBM48 (Two-hybrid)

ESM2 similar proteins: A4FVJ7, A6QPE1, E7F7X0, F1Q8J0, O43683, O60566, P92204, Q08AZ1, Q0VBD2, Q32NQ8, Q3MHP0, Q3UZ01, Q4G055, Q4R707, Q561R3, Q5F3D1, Q5HZN1, Q5R4U2, Q5R6C7, Q5R789, Q5RL73, Q5SPR8, Q5ZIX8, Q6DD45, Q6DE94, Q6DJS0, Q6GQJ2, Q6IE81, Q6IRB8, Q6NZY4, Q6P2L6, Q6XV80, Q6ZPI0, Q76FK4, Q7L590, Q7ZVP1, Q7ZXG4, Q801E2, Q8JZV4, Q8K298

Diamond homologs: A4FVJ7, A6QPE1, Q561R3, Q5R4U2, Q5RL73, Q8K2X2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 75 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
Transcriptional Regulation by TP53	7	9.1×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
regulation of G1/S transition of mitotic cell cycle	5	22.5×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	56
Likely benign	10
Benign	13

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
548642	NM_032120.4(RBM48):c.835A>G (p.Thr279Ala)	Likely pathogenic

SpliceAI

594 predictions. Top by Δscore:

Variant	Effect	Δscore
7:92529626:G:GT	donor_gain	1.0000
7:92532398:A:AG	acceptor_gain	1.0000
7:92532399:T:G	acceptor_gain	1.0000
7:92532400:TCA:T	acceptor_loss	1.0000
7:92532401:CA:C	acceptor_loss	1.0000
7:92532402:A:AC	acceptor_loss	1.0000
7:92532402:A:AG	acceptor_gain	1.0000
7:92532402:AG:A	acceptor_gain	1.0000
7:92532403:G:GT	acceptor_gain	1.0000
7:92532403:GG:G	acceptor_gain	1.0000
7:92532403:GGAC:G	acceptor_gain	1.0000
7:92532403:GGACA:G	acceptor_gain	1.0000
7:92532515:G:GT	donor_gain	1.0000
7:92532519:GCA:G	donor_gain	1.0000
7:92532526:T:TA	donor_gain	1.0000
7:92532527:A:AA	donor_gain	1.0000
7:92536549:G:GG	donor_gain	1.0000
7:92536847:TTA:T	acceptor_loss	1.0000
7:92536848:TAG:T	acceptor_loss	1.0000
7:92536850:G:GA	acceptor_loss	1.0000
7:92536850:GGTA:G	acceptor_gain	1.0000
7:92529470:TTTCA:T	acceptor_loss	0.9900
7:92529471:TTCAG:T	acceptor_loss	0.9900
7:92529473:CA:C	acceptor_loss	0.9900
7:92529474:A:AT	acceptor_loss	0.9900
7:92529475:GGTAT:G	acceptor_gain	0.9900
7:92529663:CAAGG:C	donor_loss	0.9900
7:92529666:GGT:G	donor_loss	0.9900
7:92529667:G:C	donor_loss	0.9900
7:92529668:T:G	donor_loss	0.9900

AlphaMissense

2408 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:92532413:G:C	K104N	0.998
7:92532413:G:T	K104N	0.998
7:92529636:T:C	L91P	0.997
7:92529498:C:T	S45F	0.996
7:92529620:T:C	F86L	0.996
7:92529622:T:A	F86L	0.996
7:92529622:T:G	F86L	0.996
7:92532409:C:A	A103D	0.996
7:92529497:T:C	S45P	0.995
7:92529513:T:A	I50K	0.995
7:92529645:T:C	F94S	0.995
7:92532466:C:A	A122D	0.995
7:92529632:T:G	Y90D	0.994
7:92529507:T:C	L48S	0.993
7:92529522:T:A	V53D	0.993
7:92529644:T:C	F94L	0.993
7:92529646:T:A	F94L	0.993
7:92529646:T:G	F94L	0.993
7:92532457:T:A	V119E	0.993
7:92529503:T:G	Y47D	0.992
7:92529513:T:G	I50R	0.992
7:92532451:T:A	L117H	0.992
7:92528892:T:C	Y27H	0.991
7:92529639:T:A	I92N	0.991
7:92532404:G:C	R101S	0.991
7:92532404:G:T	R101S	0.991
7:92532435:T:C	F112L	0.991
7:92532437:C:A	F112L	0.991
7:92532437:C:G	F112L	0.991
7:92532453:C:G	H118D	0.991

dbSNP variants (sampled 300 via entrez): RS1000014747 (7:92537605 A>G), RS1000317139 (7:92539844 C>G), RS1000490837 (7:92537842 T>A), RS1000791010 (7:92529341 T>G), RS1000885834 (7:92529557 C>A,G), RS1000961060 (7:92533786 A>G), RS1001016310 (7:92533989 AC>A), RS1001035485 (7:92540156 A>G), RS1001092109 (7:92539128 A>T), RS1001231526 (7:92534341 G>A), RS1001240192 (7:92527023 G>C,T), RS1001461533 (7:92538823 C>G), RS1003017067 (7:92530933 C>G,T), RS1003074677 (7:92539712 C>T), RS1003129252 (7:92537747 C>G,T)

Disease associations

OMIM: gene MIM:621015 | disease phenotypes: MIM:256100

GenCC curated gene-disease

Mondo (1): nephronophthisis (MONDO:0019005)

Orphanet (1): Nephronophthisis (Orphanet:655)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000090	Nephronophthisis

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST005588_34	Idiopathic dilated cardiomyopathy	7.000000e-06
GCST012227_124	Hip circumference adjusted for BMI	1.000000e-10
GCST90020028_173	Hip circumference adjusted for BMI	2.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009094	idiopathic dilated cardiomyopathy
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	3
Air Pollutants	affects expression, increases abundance, decreases expression	2
Formaldehyde	decreases expression, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
methylmercuric chloride	decreases expression	1
propionaldehyde	decreases expression	1
lei gong teng	increases expression	1
epigallocatechin gallate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
MT19c compound	increases expression	1
Leflunomide	increases expression	1
Arsenic	increases abundance, increases expression	1
Cisplatin	decreases expression, affects cotreatment	1
Coal	increases abundance, decreases expression	1
Copper	affects binding, decreases expression	1
Disulfiram	decreases expression, affects binding	1
Folic Acid	decreases expression	1
Hydrogen Peroxide	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Phenylmercuric Acetate	decreases expression	1
Smoke	decreases expression, increases abundance	1
Urethane	affects expression	1
Acrylamide	increases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01022957	Not specified	COMPLETED	Nephronophthisis : Clinical and Genetic Study
NCT01401998	Not specified	RECRUITING	ARPKD Database Study
NCT04874909	Not specified	COMPLETED	Classification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT05286632	Not specified	COMPLETED	KidneYou - Innovative Digital Therapy
NCT06065852	Not specified	RECRUITING	National Registry of Rare Kidney Diseases
NCT06648044	Not specified	RECRUITING	Research of Therapeutic Targets in the Frame of Nephronophthisis and Renal Associated Ciliopathies