RBM12B

gene
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Summary

RBM12B (RNA binding motif protein 12B, HGNC:32310) is a protein-coding gene on chromosome 8q22.1, encoding RNA-binding protein 12B (Q8IXT5).

Enables RNA binding activity. Predicted to be involved in regulation of RNA splicing. Predicted to be part of ribonucleoprotein complex. Predicted to be active in nucleoplasm.

Source: NCBI Gene 389677 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 165 total
  • Druggable target: yes
  • MANE Select transcript: NM_001377960

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:32310
Approved symbolRBM12B
NameRNA binding motif protein 12B
Location8q22.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000183808
Ensembl biotypeprotein_coding
Entrez389677

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 25 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000399300, ENST00000517700, ENST00000518597, ENST00000519109, ENST00000520560, ENST00000520961, ENST00000891584, ENST00000891585, ENST00000891586, ENST00000891587, ENST00000891588, ENST00000891589, ENST00000891590, ENST00000891591, ENST00000891592, ENST00000891593, ENST00000932408, ENST00000932409, ENST00000932410, ENST00000932411, ENST00000932412, ENST00000932413, ENST00000932414, ENST00000932415, ENST00000963705, ENST00000963706

RefSeq mRNA: 6 — MANE Select: NM_001377960 NM_001377960, NM_001377961, NM_001377962, NM_001377963, NM_001377964, NM_203390

CCDS: CCDS43755

Canonical transcript exons

ENST00000520560 — 4 exons

ExonStartEnd
ENSE000015373969372815593736438
ENSE000015373979373730793737355
ENSE000020962899374062993740696
ENSE000021113169374088193741009

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 91.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.0040 / max 618.1161, expressed in 1806 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
939689.94781709
939698.52001755
939652.19361093
939701.0358609
939670.8393495
939660.4674251

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370191.94gold quality
adrenal tissueUBERON:001830390.82gold quality
caput epididymisUBERON:000435888.90gold quality
corpus epididymisUBERON:000435988.76gold quality
buccal mucosa cellCL:000233687.78gold quality
tendonUBERON:000004386.93gold quality
ganglionic eminenceUBERON:000402386.48gold quality
cauda epididymisUBERON:000436086.46gold quality
ventricular zoneUBERON:000305385.98gold quality
colonic epitheliumUBERON:000039784.98gold quality
cortical plateUBERON:000534384.94gold quality
endothelial cellCL:000011584.80gold quality
superficial temporal arteryUBERON:000161484.69gold quality
ovaryUBERON:000099284.63gold quality
left ovaryUBERON:000211984.63gold quality
sural nerveUBERON:001548884.08gold quality
lymph nodeUBERON:000002983.90gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.44gold quality
endometriumUBERON:000129583.21gold quality
right ovaryUBERON:000211882.85gold quality
corpus callosumUBERON:000233682.31gold quality
rectumUBERON:000105281.93gold quality
body of uterusUBERON:000985381.92gold quality
islet of LangerhansUBERON:000000681.77gold quality
vermiform appendixUBERON:000115481.74gold quality
embryoUBERON:000092281.56gold quality
stromal cell of endometriumCL:000225581.44gold quality
endocervixUBERON:000045881.05gold quality
mammary ductUBERON:000176580.58gold quality
leukocyteCL:000073880.54gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

133 targeting RBM12B, 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-3163100.0077.238605
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5692A100.0074.406850
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-196A-5P100.0068.16684
HSA-MIR-196B-5P100.0068.16681
HSA-MIR-6759-5P99.9966.54785
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-477599.9875.006394
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-548P99.9872.253784
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-302E99.9670.742669
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_reriorbm12baENSDARG00000055889
danio_reriorbm12bbENSDARG00000079717
mus_musculusRbm12b1ENSMUSG00000046667
mus_musculusRbm12b2ENSMUSG00000052137
rattus_norvegicusRbm12bENSRNOG00000016330
rattus_norvegicusLOC120102832ENSRNOG00000055292
drosophila_melanogasterfusFBGN0023441
drosophila_melanogastergloFBGN0259139
caenorhabditis_elegansWBGENE00006367
caenorhabditis_elegansrbm-12WBGENE00013703
caenorhabditis_elegansWBGENE00022253

Paralogs (8): HNRNPH3 (ENSG00000096746), ESRP2 (ENSG00000103067), ESRP1 (ENSG00000104413), HNRNPH2 (ENSG00000126945), GRSF1 (ENSG00000132463), HNRNPH1 (ENSG00000169045), HNRNPF (ENSG00000169813), RBM12 (ENSG00000244462)

Protein

Protein identifiers

RNA-binding protein 12BQ8IXT5 (reviewed: Q8IXT5)

Alternative names: RNA-binding motif protein 12B

All UniProt accessions (5): B9ZVT1, E5RHG1, E5RJ83, E5RJV8, Q8IXT5

RefSeq proteins (6): NP_001364889, NP_001364890, NP_001364891, NP_001364892, NP_001364893, NP_976324 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR034588RBM12B_RRM2Domain
IPR034858RBM12B_RRM3Domain
IPR035979RBD_domain_sfHomologous_superfamily
IPR047188RRM4_RBM12BDomain
IPR050666ESRPFamily

Pfam: PF00076

UniProt features (40 total): modified residue 18, cross-link 6, domain 4, compositionally biased region 4, region of interest 4, sequence variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IXT5-F156.090.11

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 (24): 98, 101, 112, 250, 254, 276, 278, 280, 292, 294, 319, 377, 575, 591, 638, 640, 710, 718, 114, 151 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): PATIL_LIVER_CANCER, GOBP_RNA_SPLICING, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, chr8q22, GTGACTT_MIR224, GOBP_REGULATION_OF_RNA_SPLICING, TGGAAA_NFAT_Q4_01, GOCC_RIBONUCLEOPROTEIN_COMPLEX, MMEF2_Q6, STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP, PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7, STAT6_01, DURAND_STROMA_NS_UP, ZWANG_EGF_INTERVAL_UP, FOXN3_TARGET_GENES

GO Biological Process (1): regulation of RNA splicing (GO:0043484)

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

GO Cellular Component (2): nucleoplasm (GO:0005654), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
RNA splicing1
regulation of gene expression1
regulation of primary metabolic process1
nucleic acid binding1
nuclear lumen1
cellular anatomical structure1
protein-containing complex1

Protein interactions and networks

STRING

1158 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RBM12BTSKSQ9UJT2590
RBM12BTRABDQ9H4I3504
RBM12BTBC1D22AQ8WUA7491
RBM12BYLPM1P49750473
RBM12BTHAP2Q9H0W7446
RBM12BSLCO6A1Q86UG4418
RBM12BC6orf120Q7Z4R8373
RBM12BTMEM68Q96MH6371
RBM12BZNF253O75346366
RBM12BMTCL1Q9Y4B5358
RBM12BASB12Q8WXK4352
RBM12BC11orf96Q7Z7L8348
RBM12BNHLRC3Q5JS37340
RBM12BCOPS7BQ9H9Q2340
RBM12BDAD1P46966329

IntAct

44 interactions, top by confidence:

ABTypeScore
HNRNPH2PLOD2psi-mi:“MI:0914”(association)0.530
RBM12BCACNA1Apsi-mi:“MI:0915”(physical association)0.510
RBMXRBM12Bpsi-mi:“MI:0915”(physical association)0.400
Racgap1DDX3Xpsi-mi:“MI:0914”(association)0.350
Taf15BTBD10psi-mi:“MI:0914”(association)0.350
Ctnnbl1LCMT2psi-mi:“MI:0914”(association)0.350
MATR3BCLAF3psi-mi:“MI:0914”(association)0.350
HNRNPA1MATR3psi-mi:“MI:0914”(association)0.350
Slain1OARD1psi-mi:“MI:0914”(association)0.350
Hnrnpa3MATR3psi-mi:“MI:0914”(association)0.350
FusDDX3Xpsi-mi:“MI:0914”(association)0.350
PPP1CCCLIC1psi-mi:“MI:0914”(association)0.350
PPP1CBPLEKHG3psi-mi:“MI:0914”(association)0.350
Srsf1SRRM1psi-mi:“MI:0914”(association)0.350
RRP1BZNF785psi-mi:“MI:0914”(association)0.350
AURKBHSP90AA1psi-mi:“MI:0914”(association)0.350
repVWA8psi-mi:“MI:0914”(association)0.350
MAP1LC3Apsi-mi:“MI:0914”(association)0.350
CASP8CCN1psi-mi:“MI:0914”(association)0.350
RB1ZNF593psi-mi:“MI:0914”(association)0.350
SHANK3IGKV3D-15psi-mi:“MI:0914”(association)0.350
DYRK1ATEX13Dpsi-mi:“MI:0914”(association)0.350
RBM12BRNF40psi-mi:“MI:0914”(association)0.350
POMGNT2FAM83Gpsi-mi:“MI:0914”(association)0.350
SF3B1RBM10psi-mi:“MI:0914”(association)0.350
ATF3C11orf98psi-mi:“MI:0914”(association)0.350
GATA2C11orf98psi-mi:“MI:0914”(association)0.350
CTNNA1EFCAB5psi-mi:“MI:0914”(association)0.350

BioGRID (101): RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Proximity Label-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS), RBM12B (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YWL9, A0A0J9YY54, A0A1D9BZF0, A0A494C071, A6NDE4, A6NEQ0, A6QL64, A8MQ14, B3KS81, E9Q6E9, O77733, P05995, P0C7P1, P0C8Z4, P0DJD3, P0DJD4, P0DKJ7, P0DKJ8, P0DKL2, P0DPF3, P11088, P18751, P18753, P20930, P97347, Q15415, Q2VIS4, Q3BBV2, Q42626, Q5D862, Q5HY64, Q5JPF3, Q5U7M9, Q6JHY2, Q6P3W6, Q6XPR3, Q86T75, Q86VE3, Q86YZ3, Q8IXT5

Diamond homologs: A1L1G1, A8WPC5, B2RYD2, B2RYJ8, O35737, P31942, P31943, P52597, P55795, P70333, Q12849, Q22708, Q3SZF3, Q3US41, Q5E9J1, Q5RD26, Q5RFT7, Q60HC3, Q6AY09, Q6DEZ7, Q6NXG1, Q794E4, Q7ZY29, Q8C5Q4, Q8IXT5, Q8K0G8, Q8R3C6, Q8VHV7, Q9Y4C8, Q9Z2X1, Q15020, Q5REG1, Q5ZLR4, Q5RBM8, Q66JV4, Q80YR9, Q8R4X3, Q8SQ27, Q9NTZ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 66 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
mRNA 3’-end processing525.2×8e-05
mRNA Polyadenylation1022.5×4e-09
Transport of Mature mRNA derived from an Intron-Containing Transcript519.5×2e-04
Processing of Capped Intron-Containing Pre-mRNA919.0×7e-08
mRNA Splicing616.9×8e-05
mRNA Splicing - Major Pathway1115.4×1e-08
Dengue Virus-Host Interactions1011.7×6e-07
Metabolism of RNA66.4×7e-03

GO biological processes:

GO termPartnersFoldFDR
regulation of alternative mRNA splicing, via spliceosome523.5×2e-04
mRNA splicing, via spliceosome1119.4×4e-09
RNA splicing915.3×2e-06
mRNA processing812.1×5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance150
Likely benign11
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1022 predictions. Top by Δscore:

VariantEffectΔscore
8:93737351:CTTAA:Cacceptor_gain1.0000
8:93737352:TTAA:Tacceptor_gain1.0000
8:93737356:C:CCacceptor_gain1.0000
8:93728203:A:AGacceptor_gain0.9900
8:93728204:G:GGacceptor_gain0.9900
8:93728204:GGT:Gacceptor_gain0.9900
8:93737353:TAA:Tacceptor_gain0.9900
8:93740861:A:ACdonor_gain0.9900
8:93740862:C:CCdonor_gain0.9900
8:93740878:CACCA:Cdonor_gain0.9900
8:93740880:CCA:Cdonor_gain0.9900
8:93733728:TGCC:Tdonor_gain0.9800
8:93738823:CA:Cdonor_gain0.9700
8:93740880:C:CTdonor_gain0.9700
8:93736369:C:Tacceptor_gain0.9600
8:93740900:A:Tdonor_gain0.9600
8:93728201:A:Gacceptor_gain0.9500
8:93733727:TTGC:Tdonor_gain0.9500
8:93736435:TGACC:Tacceptor_loss0.9500
8:93736436:GACC:Gacceptor_loss0.9500
8:93736439:C:CAacceptor_loss0.9500
8:93736440:T:Gacceptor_loss0.9500
8:93737305:ACC:Aacceptor_loss0.9500
8:93737355:AC:Aacceptor_loss0.9500
8:93737356:C:Gacceptor_loss0.9500
8:93737357:T:Aacceptor_loss0.9500
8:93740624:TATAC:Tdonor_loss0.9500
8:93740625:ATAC:Adonor_loss0.9500
8:93740626:TA:Tdonor_loss0.9500
8:93740627:ACC:Adonor_loss0.9500

AlphaMissense

785 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:93736245:C:GA56P0.997
8:93736244:G:TA56D0.996
8:93736270:A:CF47L0.996
8:93736270:A:TF47L0.996
8:93736272:A:GF47L0.996
8:93736284:C:GA43P0.996
8:93736254:C:GA53P0.995
8:93736271:A:GF47S0.995
8:93736279:A:CF44L0.995
8:93736279:A:TF44L0.995
8:93736281:A:GF44L0.995
8:93736394:C:GR6P0.995
8:93736189:A:CS74R0.994
8:93736189:A:TS74R0.994
8:93736191:T:GS74R0.994
8:93736199:A:GL71P0.994
8:93736382:A:GL10P0.994
8:93736253:G:TA53E0.993
8:93736328:A:TI28N0.991
8:93736343:A:GF23S0.991
8:93736352:C:GR20P0.991
8:93736400:A:TV4D0.991
8:93736249:T:AR54S0.990
8:93736249:T:GR54S0.990
8:93736391:A:GL7S0.990
8:93736247:C:GR55P0.989
8:93736328:A:CI28S0.989
8:93736271:A:CF47C0.988
8:93736277:A:TI45N0.988
8:93736283:G:TA43D0.988

dbSNP variants (sampled 300 via entrez): RS1000012792 (8:93731513 A>C), RS1000019856 (8:93739968 A>G), RS1000154700 (8:93733051 GAA>G,GA,GAAA), RS1000218085 (8:93734570 G>A,C), RS1000436730 (8:93741060 A>C,G), RS1001468709 (8:93738763 G>GT), RS1001712613 (8:93742414 C>G,T), RS1001845687 (8:93736422 A>G), RS1001888276 (8:93736084 A>C), RS1002118153 (8:93729516 T>C), RS1002164814 (8:93742072 T>C), RS1002256822 (8:93732875 G>GT), RS1002509829 (8:93739629 C>G,T), RS1002656135 (8:93731099 G>A), RS1002786082 (8:93732633 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): myoepithelial tumor (MONDO:0002380)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D009208MyoepitheliomaC04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6196110 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, decreases methylation4
trichostatin Aaffects cotreatment, decreases expression2
sodium arsenitedecreases expression, affects cotreatment, increases abundance2
Arsenicaffects methylation, affects cotreatment, decreases expression, increases abundance2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Rotenonedecreases expression2
Cadmium Chlorideincreases expression, decreases expression, increases abundance2
aristolochic acid Idecreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4decreases expression1
FR900359affects phosphorylation1
TAK-243decreases sumoylation1
triphenyl phosphateaffects expression1
bisphenol Aincreases methylation1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
coumarinaffects phosphorylation1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
deguelindecreases expression1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamidedecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001increases expression1
dorsomorphinaffects cotreatment, decreases expression1
fatostatindecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Resveratrolaffects cotreatment, increases expression1
Leflunomidedecreases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumincreases abundance, increases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL6096343BindingBinding affinity to RBM12B at C204 residue in human MDA-MB-231 cells at 1 uM incubated for 3 hrs in presence of IAA by proteome-wide scale isoTOP ABPP methodCovalent Inhibitors of KEAP1 with Exquisite Selectivity. — J Med Chem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03600649PHASE1UNKNOWNClinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196PHASE1/PHASE2UNKNOWNA Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272PHASE1/PHASE2RECRUITINGNRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190PHASE1/PHASE2RECRUITINGAlpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420Not specifiedCOMPLETEDMalignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): myoepithelial tumor