RBM43

Summary

RBM43 (RNA binding motif protein 43, HGNC:24790) is a protein-coding gene on chromosome 2q23.3, encoding RNA-binding protein 43 (Q6ZSC3).

Predicted to enable RNA binding activity.

Source: NCBI Gene 375287 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_198557

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24790
Approved symbol	RBM43
Name	RNA binding motif protein 43
Location	2q23.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ45645
Ensembl gene	ENSG00000184898
Ensembl biotype	protein_coding
Entrez	375287

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000331426, ENST00000409092

RefSeq mRNA: 1 — MANE Select: NM_198557 NM_198557

CCDS: CCDS2191

Canonical transcript exons

ENST00000331426 — 4 exons

Exon	Start	End
ENSE00001295653	151247940	151251664
ENSE00001303616	151252755	151252855
ENSE00001322411	151255533	151255743
ENSE00001365051	151261725	151261863

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 85.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1961 / max 81.2498, expressed in 1605 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
31104	3.6554	1366
31105	1.5407	1030

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	85.90	gold quality
calcaneal tendon	UBERON:0003701	81.27	gold quality
fallopian tube	UBERON:0003889	80.50	gold quality
right uterine tube	UBERON:0001302	79.25	gold quality
left adrenal gland	UBERON:0001234	79.15	gold quality
right adrenal gland cortex	UBERON:0035827	79.12	gold quality
right adrenal gland	UBERON:0001233	78.80	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.63	gold quality
bronchial epithelial cell	CL:0002328	78.61	gold quality
left adrenal gland cortex	UBERON:0035825	78.61	gold quality
adrenal gland	UBERON:0002369	78.60	gold quality
gall bladder	UBERON:0002110	78.49	gold quality
adrenal cortex	UBERON:0001235	78.42	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.26	gold quality
adrenal tissue	UBERON:0018303	78.22	gold quality
smooth muscle tissue	UBERON:0001135	78.02	gold quality
right coronary artery	UBERON:0001625	77.72	gold quality
stromal cell of endometrium	CL:0002255	77.69	gold quality
bronchus	UBERON:0002185	77.68	gold quality
colonic epithelium	UBERON:0000397	77.49	gold quality
descending thoracic aorta	UBERON:0002345	77.19	gold quality
parietal pleura	UBERON:0002400	77.19	gold quality
visceral pleura	UBERON:0002401	76.68	gold quality
monocyte	CL:0000576	76.07	gold quality
ovary	UBERON:0000992	76.07	gold quality
left ovary	UBERON:0002119	76.03	gold quality
leukocyte	CL:0000738	76.02	gold quality
caput epididymis	UBERON:0004358	75.79	gold quality
tibial nerve	UBERON:0001323	75.78	gold quality
lymph node	UBERON:0000029	75.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting RBM43, 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-6798-5P	100.00	65.77	699
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-371B-5P	99.99	75.34	4759
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-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-92A-2-5P	99.75	67.01	2164

Literature-anchored findings (GeneRIF, showing 1)

• RNA-binding motif protein 43 (RBM43) suppresses hepatocellular carcinoma progression through modulation of cyclin B1 expression. (PMID:32632220)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rbm43	ENSMUSG00000036249
rattus_norvegicus	Rbm43	ENSRNOG00000077161

Paralogs (2): IFI35 (ENSG00000068079), NMI (ENSG00000123609)

Protein

Protein identifiers

RNA-binding protein 43 — Q6ZSC3 (reviewed: Q6ZSC3)

Alternative names: RNA-binding motif protein 43

All UniProt accessions (2): B8ZZQ2, Q6ZSC3

RefSeq proteins (1): NP_940959* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily

UniProt features (3 total): chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZSC3-F1	77.12	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN, GSE13522_WT_VS_IFNG_KO_SKIN_DN, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, BRUINS_UVC_RESPONSE_MIDDLE, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, ESC_V6.5_UP_LATE.V1_DN, FOXE1_TARGET_GENES, PCGF1_TARGET_GENES, ZIM3_TARGET_GENES, ZNF407_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
nucleic acid binding	1

Protein interactions and networks

STRING

504 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM43	RND3	P52199	725
RBM43	FAM117B	Q6P1L5	483
RBM43	IQSEC3	Q9UPP2	482
RBM43	RNF144B	Q7Z419	466
RBM43	EFCAB11	Q9BUY7	440
RBM43	ZC3HAV1L	Q96H79	426
RBM43	TARDBP	Q13148	419
RBM43	RPP25	Q9BUL9	401
RBM43	RBM8A	Q9Y5S9	368
RBM43	TCERG1L	Q5VWI1	350
RBM43	TMCO5A	Q8N6Q1	343
RBM43	TENT5B	Q96A09	330
RBM43	VEZT	Q9HBM0	323
RBM43	GALNT18	Q6P9A2	321
RBM43	MGAT4C	Q9UBM8	321

IntAct

12 interactions, top by confidence:

A	B	Type	Score
IKZF1	RBM43	psi-mi:“MI:0915”(physical association)	0.560
DAZAP2	RBM43	psi-mi:“MI:0915”(physical association)	0.560
ESR2		psi-mi:“MI:0914”(association)	0.350
FTL	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
RBM43	MAPKAPK2	psi-mi:“MI:0914”(association)	0.350
FTL		psi-mi:“MI:0914”(association)	0.350
RBM43	DAZAP2	psi-mi:“MI:0915”(physical association)	0.000
RBM43	IKZF1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): RBM43 (Affinity Capture-MS), RBM43 (Two-hybrid), IKZF1 (Two-hybrid), MAPK14 (Affinity Capture-MS), PARP9 (Affinity Capture-MS), DTX3L (Affinity Capture-MS), ARHGAP8 (Affinity Capture-MS), RBM43 (Affinity Capture-MS), MAPKAPK2 (Affinity Capture-MS), RBM43 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LIF8, A0A2P1BRP3, A0A386CAB9, A0JN92, A1A4Y4, O14791, P27473, P59045, P86448, P86449, Q0GUM3, Q13075, Q3B7D9, Q3T9E4, Q3TL54, Q53G44, Q5NCI0, Q5RFJ8, Q60766, Q62293, Q66X01, Q66X03, Q66X05, Q66X22, Q6AYC2, Q6ZSC3, Q7Z745, Q84WJ0, Q86W28, Q8BV66, Q8BVM9, Q8C6J9, Q8CBA2, Q8CCN1, Q8TCB0, Q8TCY9, Q8TD90, Q90597, Q99388, Q99J64

Diamond homologs: Q3B7D9, Q6ZSC3, Q99J64

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

662 predictions. Top by Δscore:

Variant	Effect	Δscore
2:151255530:TAC:T	donor_loss	1.0000
2:151255531:A:C	donor_loss	1.0000
2:151255532:CC:C	donor_loss	1.0000
2:151255550:A:AC	donor_gain	1.0000
2:151255565:C:A	donor_gain	1.0000
2:151255565:C:CA	donor_loss	1.0000
2:151255566:C:A	donor_gain	1.0000
2:151255740:ATGC:A	acceptor_gain	1.0000
2:151255741:TGC:T	acceptor_gain	1.0000
2:151255742:GCC:G	acceptor_loss	1.0000
2:151255743:CCTG:C	acceptor_loss	1.0000
2:151255744:C:CC	acceptor_gain	1.0000
2:151255744:CT:C	acceptor_loss	1.0000
2:151255745:T:A	acceptor_loss	1.0000
2:151255555:A:C	donor_gain	0.9900
2:151255739:GATGC:G	acceptor_gain	0.9900
2:151255741:TGCC:T	acceptor_gain	0.9900
2:151255742:GC:G	acceptor_gain	0.9900
2:151255742:GCCT:G	acceptor_gain	0.9900
2:151255743:CC:C	acceptor_gain	0.9900
2:151255743:CCTGT:C	acceptor_gain	0.9900
2:151255744:C:A	acceptor_gain	0.9900
2:151252856:C:CC	acceptor_gain	0.9800
2:151255586:A:AC	donor_gain	0.9800
2:151255740:ATGCC:A	acceptor_gain	0.9800
2:151255745:T:G	acceptor_gain	0.9800
2:151255746:G:GC	acceptor_gain	0.9800
2:151251522:T:TA	donor_gain	0.9700
2:151254855:C:CT	donor_gain	0.9700
2:151255533:C:G	donor_loss	0.9700

AlphaMissense

2346 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:151255546:G:C	F67L	0.958
2:151255546:G:T	F67L	0.958
2:151255548:A:G	F67L	0.958
2:151250973:C:T	G336E	0.950
2:151251585:A:G	L132P	0.950
2:151251520:C:G	G154R	0.940
2:151251520:C:T	G154R	0.940
2:151251623:A:C	F119L	0.935
2:151251623:A:T	F119L	0.935
2:151251625:A:G	F119L	0.935
2:151251299:A:C	F227L	0.925
2:151251299:A:T	F227L	0.925
2:151251301:A:G	F227L	0.925
2:151255559:G:T	A63E	0.925
2:151255627:G:C	F40L	0.923
2:151255627:G:T	F40L	0.923
2:151255629:A:G	F40L	0.923
2:151255547:A:G	F67S	0.916
2:151251557:G:C	F141L	0.913
2:151251557:G:T	F141L	0.913
2:151251559:A:G	F141L	0.913
2:151251495:A:G	L162P	0.910
2:151255553:A:T	V65E	0.910
2:151251295:A:C	Y229D	0.908
2:151251519:C:T	G154E	0.899
2:151250974:C:G	G336R	0.898
2:151250974:C:T	G336R	0.898
2:151251512:A:C	F156L	0.897
2:151251512:A:T	F156L	0.897
2:151251514:A:G	F156L	0.897

dbSNP variants (sampled 300 via entrez): RS1000204749 (2:151259051 G>A), RS1000315632 (2:151252978 A>G), RS1000324954 (2:151259384 G>A), RS1000334202 (2:151252991 A>C), RS1000347460 (2:151259852 C>A), RS1001053026 (2:151263758 A>G), RS1001092907 (2:151258392 A>C), RS1001371279 (2:151252677 T>C,G), RS1001953869 (2:151253082 G>A), RS1002017591 (2:151253616 T>C), RS1002034658 (2:151263695 G>A), RS1002064929 (2:151259922 G>A,C), RS1002118639 (2:151259647 T>A,C), RS1002555022 (2:151254725 G>A,T), RS1002733056 (2:151247938 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

8 associations (top):

Study	Trait	p-value
GCST001369_2	Type 2 diabetes	7.000000e-09
GCST001894_3	Endometriosis	6.000000e-08
GCST004574_1	Skin aging (microtopography measurement)	2.000000e-06
GCST005651_3	Urinary metabolite levels in chronic kidney disease	4.000000e-08
GCST006493_8	Systemic sclerosis	7.000000e-06
GCST006531_1	Esophageal adenocarcinoma x gastroesophageal reflux disease interaction	2.000000e-07
GCST009391_170	Metabolite levels	8.000000e-06
GCST011494_13	Daytime nap	4.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005116	urinary metabolite measurement
EFO:0009768	glutamine measurement
EFO:0007828	daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression	5
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Air Pollutants	decreases expression, increases abundance	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Particulate Matter	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
trichostatin A	increases expression	1
arsenite	affects binding, decreases reaction	1
butyraldehyde	decreases expression	1
zinc chromate	increases abundance, increases expression	1
chromium hexavalent ion	increases abundance, 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
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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