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RBM42

gene
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Also known as MGC10433

Summary

RBM42 (RNA binding motif protein 42, HGNC:28117) is a protein-coding gene on chromosome 19q13.12, encoding RNA-binding protein 42 (Q9BTD8). Binds (via the RRM domain) to the 3’-untranslated region (UTR) of CDKN1A mRNA. It is a selective cancer dependency (DepMap: 73.8% of cell lines).

Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within negative regulation of mRNA splicing, via spliceosome. Part of U4/U6 x U5 tri-snRNP complex.

Source: NCBI Gene 79171 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 57 total
  • Cancer dependency (DepMap): dependent in 73.8% of screened cell lines
  • MANE Select transcript: NM_024321

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28117
Approved symbolRBM42
NameRNA binding motif protein 42
Location19q13.12
Locus typegene with protein product
StatusApproved
AliasesMGC10433
Ensembl geneENSG00000126254
Ensembl biotypeprotein_coding
OMIM613232
Entrez79171

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 19 protein_coding, 1 retained_intron

ENST00000262633, ENST00000586618, ENST00000588161, ENST00000589559, ENST00000589871, ENST00000592202, ENST00000592526, ENST00000907957, ENST00000907958, ENST00000907959, ENST00000907960, ENST00000907961, ENST00000907962, ENST00000934967, ENST00000934968, ENST00000943047, ENST00000943048, ENST00000943049, ENST00000943050, ENST00000943051

RefSeq mRNA: 2 — MANE Select: NM_024321 NM_001319113, NM_024321

CCDS: CCDS12468

Canonical transcript exons

ENST00000262633 — 10 exons

ExonStartEnd
ENSE000006999563563368735634019
ENSE000006999573563307735633252
ENSE000008627983563133135631405
ENSE000008627993563293635633001
ENSE000008956343563425635634373
ENSE000010571903563715835637352
ENSE000028632553562903635629281
ENSE000035469393563114035631224
ENSE000036338283562952035629673
ENSE000038445813563744235637685

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 95.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 53.8534 / max 400.3973, expressed in 1826 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
17535632.14801822
17535719.72511815
1753581.1424596
1753550.8380573

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
mucosa of transverse colonUBERON:000499195.23gold quality
lower esophagus muscularis layerUBERON:003583395.16gold quality
lower esophagusUBERON:001347395.15gold quality
popliteal arteryUBERON:000225095.01gold quality
tibial arteryUBERON:000761095.00gold quality
esophagogastric junction muscularis propriaUBERON:003584194.94gold quality
aortaUBERON:000094794.81gold quality
skin of legUBERON:000151194.80gold quality
left uterine tubeUBERON:000130394.77gold quality
thoracic aortaUBERON:000151594.67gold quality
ascending aortaUBERON:000149694.65gold quality
apex of heartUBERON:000209894.65gold quality
muscle layer of sigmoid colonUBERON:003580594.64gold quality
ectocervixUBERON:001224994.61gold quality
body of uterusUBERON:000985394.54gold quality
left coronary arteryUBERON:000162694.46gold quality
right coronary arteryUBERON:000162594.37gold quality
endocervixUBERON:000045894.35gold quality
descending thoracic aortaUBERON:000234594.34gold quality
coronary arteryUBERON:000162194.27gold quality
right ovaryUBERON:000211894.24gold quality
C1 segment of cervical spinal cordUBERON:000646994.12gold quality
peripheral nervous systemUBERON:000001094.11gold quality
nerveUBERON:000102194.11gold quality
tibial nerveUBERON:000132394.11gold quality
skin of abdomenUBERON:000141694.08gold quality
hindlimb stylopod muscleUBERON:000425294.08gold quality
mucosa of stomachUBERON:000119994.05gold quality
granulocyteCL:000009494.01gold quality
gastrocnemiusUBERON:000138894.00gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting RBM42, 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-509399.6769.262291
HSA-MIR-510-3P99.5470.062965
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-4738-3P98.9867.981846
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-426098.7865.37848
HSA-MIR-582-3P96.6967.381019
HSA-MIR-609091.0162.65222

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 73.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • hnRNP K and RBM42 have a role in the maintenance of cellular ATP level in the stress conditions possibly through protecting their target mRNAs. (PMID:19170760)
  • Biallelic variants in RBM42 cause a multisystem disorder with neurological, facial, cardiac, and musculoskeletal involvement. (PMID:37294900)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusRbm42ENSMUSG00000036733
rattus_norvegicusRbm42ENSRNOG00000024278

Protein

Protein identifiers

RNA-binding protein 42 — Q9BTD8 (reviewed: Q9BTD8)

Alternative names: RNA-binding motif protein 42

All UniProt accessions (5): Q9BTD8, K7EML2, K7EP90, K7EQ03, K7ER08

UniProt curated annotations — full annotation on UniProt →

Function. Binds (via the RRM domain) to the 3’-untranslated region (UTR) of CDKN1A mRNA.

Subunit / interactions. Interacts with HNRNPK.

Subcellular location. Nucleus. Cytoplasm.

Similarity. Belongs to the RRM RBM42 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q9BTD8-11yes
Q9BTD8-22, RBM42a
Q9BTD8-33
Q9BTD8-44, RBM42b

RefSeq proteins (2): NP_001306042, NP_077297* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR034215RBM42_RRMDomain
IPR035979RBD_domain_sfHomologous_superfamily
IPR050825RBM42_RBP45_47-likeFamily

Pfam: PF00076

UniProt features (28 total): modified residue 6, strand 6, splice variant 3, helix 3, region of interest 3, turn 2, compositionally biased region 2, initiator methionine 1, chain 1, domain 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
6QW6ELECTRON MICROSCOPY2.92
8H6EELECTRON MICROSCOPY3.2
8H6JELECTRON MICROSCOPY3.25
6QX9ELECTRON MICROSCOPY3.28
8QP8ELECTRON MICROSCOPY3.5
8QP9ELECTRON MICROSCOPY4.1
8QPKELECTRON MICROSCOPY4.2
8R0AELECTRON MICROSCOPY5.8
8R08ELECTRON MICROSCOPY6.1
8QXDELECTRON MICROSCOPY9.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BTD8-F163.470.18

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 (6): 153, 158, 168, 181, 2, 135

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-72163mRNA Splicing - Major Pathway

MSigDB gene sets: 130 (showing top): GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, MORF_PPP6C, REACTOME_MRNA_SPLICING, GOBP_REGULATION_OF_MRNA_SPLICING_VIA_SPLICEOSOME, SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC, MODULE_95, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_SPLICEOSOMAL_SNRNP_ASSEMBLY, GOBP_REGULATION_OF_RNA_SPLICING, REACTOME_METABOLISM_OF_RNA, GOCC_PRECATALYTIC_SPLICEOSOME, GOCC_SPLICEOSOMAL_TRI_SNRNP_COMPLEX

GO Biological Process (2): mRNA splicing, via spliceosome (GO:0000398), negative regulation of mRNA splicing, via spliceosome (GO:0048025)

GO Molecular Function (4): RNA binding (GO:0003723), mRNA binding (GO:0003729), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), cytoplasm (GO:0005737), U4/U6 x U5 tri-snRNP complex (GO:0046540)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
mRNA Splicing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cellular anatomical structure2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
mRNA splicing, via spliceosome1
negative regulation of RNA splicing1
regulation of mRNA splicing, via spliceosome1
negative regulation of mRNA processing1
nucleic acid binding1
RNA binding1
intracellular membrane-bounded organelle1
nuclear lumen1
nuclear protein-containing complex1
ribonucleoprotein complex1
intracellular anatomical structure1
U5 snRNP1
U4/U6 snRNP1
spliceosomal tri-snRNP complex1

Protein interactions and networks

STRING

1730 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RBM42HNRNPKP61978930
RBM42DTD2Q96FN9530
RBM42ZMAT2Q96NC0523
RBM42GRAMD1AQ96CP6516
RBM42PUF60Q9UHX1499
RBM42PRPF38AQ8NAV1497
RBM42SMU1Q2TAY7489
RBM42TMEM208Q9BTX3488
RBM42TMEM9Q9P0T7475
RBM42ERFLA0A1W2PQ73447
RBM42CCDC59Q9P031430
RBM42PRPF31Q8WWY3427
RBM42CNOT4O95628422
RBM42USP10Q14694421
RBM42FAM76AQ8TAV0419

IntAct

101 interactions, top by confidence:

ABTypeScore
SNRPEGEMIN2psi-mi:“MI:0914”(association)0.770
RBM42HNRNPKpsi-mi:“MI:0915”(physical association)0.750
HNRNPKRBM42psi-mi:“MI:0915”(physical association)0.750
PRPF3PRPF4psi-mi:“MI:0914”(association)0.730
SART1PRPF3psi-mi:“MI:0914”(association)0.720
SNRPD2GEMIN2psi-mi:“MI:0914”(association)0.710
RBM42PSMA3psi-mi:“MI:0915”(physical association)0.670
PSMA3RBM42psi-mi:“MI:0915”(physical association)0.670
LSM5LSM1psi-mi:“MI:0914”(association)0.640
SNRPBSART1psi-mi:“MI:0914”(association)0.640
PRR20DRBM42psi-mi:“MI:0915”(physical association)0.560
RBPMS2RBM42psi-mi:“MI:0915”(physical association)0.560
RBM42SNRPApsi-mi:“MI:0915”(physical association)0.550
SNRPESNRPGP15psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
KRR1MPHOSPH10psi-mi:“MI:0914”(association)0.530
SNRPEPRMT5psi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RPS3ZNF316psi-mi:“MI:0914”(association)0.530
CPSF6DDX39Apsi-mi:“MI:0914”(association)0.480
CENPLRBM42psi-mi:“MI:0915”(physical association)0.400
SLC35B3RBM42psi-mi:“MI:0915”(physical association)0.400
RBM42sctLpsi-mi:“MI:0915”(physical association)0.370
FHL3RBM42psi-mi:“MI:0915”(physical association)0.370
RBM42PPIL1psi-mi:“MI:0915”(physical association)0.370
RBM42RBM4psi-mi:“MI:0915”(physical association)0.370
RBM42RBFOX2psi-mi:“MI:0915”(physical association)0.370
ESR1ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (399): RBM42 (Two-hybrid), RBM42 (Affinity Capture-MS), RBM42 (Two-hybrid), RBM42 (Two-hybrid), RBM42 (Affinity Capture-MS), FAM103A1 (Co-fractionation), METAP1 (Co-fractionation), RBM42 (Co-fractionation), RBM42 (Co-fractionation), RBM42 (Reconstituted Complex), CAMK2G (Affinity Capture-MS), CAMK2B (Affinity Capture-MS), CAMK2D (Affinity Capture-MS), SNRNP27 (Affinity Capture-MS), RBM45 (Affinity Capture-MS)

ESM2 similar proteins: A1L020, A2VDB3, A7Z019, B7FAS0, O15047, P17678, P48634, Q01JD1, Q05A36, Q0CA78, Q0P5L0, Q1LY77, Q3TKT4, Q3UE17, Q3UH66, Q5F3P8, Q5JWF2, Q5PQQ7, Q5TM26, Q5U5Q3, Q61473, Q63803, Q66KL9, Q6AXT7, Q6DRG1, Q6MG48, Q6R0H7, Q7TSC1, Q7XT42, Q86XN8, Q8BQ89, Q8CFT2, Q8CGW4, Q8IVB5, Q8IVW6, Q8TDN4, Q91V81, Q9BQW3, Q9BTD8, Q9D1Z2

Diamond homologs: A0A0A0LLY1, A2A5N3, A2VDB3, A5A6M3, A6NDE4, A6NEQ0, D4AE41, F1QB54, F4I3B3, O60176, O64380, O75526, O93235, P0C7P1, P0C8Z4, P0CB38, P0CP46, P0CP47, P0DJD3, P0DJD4, P10979, P11940, P20965, P21187, P29341, P31483, P32588, P38159, P38760, P39684, P49310, P49311, P52912, P60824, P60825, P60826, P61286, P70318, P84586, Q00539

SIGNOR signaling

1 interactions.

AEffectBMechanism
RBM42“form complex”“U4/U6.U5 snRNP complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 100 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
Metabolism of non-coding RNA543.5×3e-06
SARS-CoV-2 modulates host translation machinery1030.7×7e-11
SARS-CoV-1 modulates host translation machinery625.4×3e-06
Eukaryotic Translation Initiation521.1×6e-05
Cap-dependent Translation Initiation521.1×6e-05
Formation of the ternary complex, and subsequently, the 43S complex720.7×2e-06
Nonsense-Mediated Decay (NMD)619.2×1e-05
Eukaryotic Translation Elongation519.1×9e-05

GO biological processes:

GO termPartnersFoldFDR
spliceosomal snRNP assembly743.7×4e-08
RNA splicing, via transesterification reactions640.3×1e-06
U2-type prespliceosome assembly533.6×3e-05
mRNA splicing, via spliceosome2019.7×7e-18
negative regulation of translation714.8×4e-05
RNA splicing1514.2×4e-11
RNA processing614.1×3e-04
regulation of alternative mRNA splicing, via spliceosome513.1×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance49
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1217 predictions. Top by Δscore:

VariantEffectΔscore
19:35629365:GAGA:Gdonor_gain1.0000
19:35629386:G:GTdonor_gain1.0000
19:35629515:TCCA:Tacceptor_loss1.0000
19:35629516:CCA:Cacceptor_loss1.0000
19:35629517:CAG:Cacceptor_loss1.0000
19:35629670:GCAG:Gdonor_gain1.0000
19:35629671:CAG:Cdonor_loss1.0000
19:35629673:GG:Gdonor_loss1.0000
19:35629674:GTA:Gdonor_loss1.0000
19:35631136:ACAG:Aacceptor_loss1.0000
19:35631137:CA:Cacceptor_loss1.0000
19:35631138:A:AGacceptor_gain1.0000
19:35631138:A:Cacceptor_loss1.0000
19:35631139:G:Aacceptor_loss1.0000
19:35631139:G:GGacceptor_gain1.0000
19:35631225:G:GAdonor_loss1.0000
19:35631226:TAA:Tdonor_loss1.0000
19:35631326:A:AGacceptor_gain1.0000
19:35631327:A:Gacceptor_gain1.0000
19:35631327:ACAG:Aacceptor_loss1.0000
19:35631328:CAGTT:Cacceptor_loss1.0000
19:35631329:A:AGacceptor_gain1.0000
19:35631329:AGTT:Aacceptor_gain1.0000
19:35631329:AGTTG:Aacceptor_gain1.0000
19:35631330:G:Aacceptor_loss1.0000
19:35631330:G:GAacceptor_gain1.0000
19:35631330:GT:Gacceptor_gain1.0000
19:35631330:GTT:Gacceptor_gain1.0000
19:35631330:GTTG:Gacceptor_gain1.0000
19:35631330:GTTGG:Gacceptor_gain1.0000

AlphaMissense

3047 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:35629268:G:CA39P1.000
19:35629651:T:AI87N1.000
19:35634319:C:AR361S1.000
19:35634319:C:GR361G1.000
19:35634320:G:CR361P1.000
19:35634326:C:AA363E1.000
19:35634329:C:AA364E1.000
19:35634340:T:AW368R1.000
19:35634340:T:CW368R1.000
19:35634341:G:CW368S1.000
19:35634342:G:CW368C1.000
19:35634342:G:TW368C1.000
19:35634346:G:AD370N1.000
19:35634346:G:CD370H1.000
19:35634347:A:GD370G1.000
19:35634347:A:TD370V1.000
19:35634352:A:CS372R1.000
19:35634354:C:AS372R1.000
19:35634354:C:GS372R1.000
19:35634356:T:CL373P1.000
19:35634364:T:AW376R1.000
19:35634364:T:CW376R1.000
19:35634365:G:CW376S1.000
19:35634365:G:TW376L1.000
19:35634366:G:CW376C1.000
19:35634366:G:TW376C1.000
19:35637160:G:TD380Y1.000
19:35637161:A:CD380A1.000
19:35637161:A:GD380G1.000
19:35637161:A:TD380V1.000

dbSNP variants (sampled 300 via entrez): RS1000042781 (19:35627353 C>A), RS1000562503 (19:35627770 C>T), RS1000656024 (19:35632315 T>C), RS1001160935 (19:35628963 TC>T,TCC), RS1001166338 (19:35628754 G>T), RS1001548827 (19:35630639 G>A), RS1001714485 (19:35637826 C>T), RS1002061874 (19:35630957 C>T), RS1002714289 (19:35635908 A>G), RS1002819234 (19:35637598 T>C), RS1002954134 (19:35629194 G>C), RS1003158431 (19:35631741 T>C), RS1003552434 (19:35627894 C>G), RS1003617760 (19:35628642 G>A), RS1003911480 (19:35633039 C>T)

Disease associations

OMIM: gene MIM:613232 | 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)

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression2
Leaddecreases expression2
aristolochic acid Iincreases expression1
ginger extractaffects expression, increases abundance, affects cotreatment1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Aaffects cotreatment, affects expression, increases abundance1
beta-lapachoneincreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
ICG 001decreases expression1
abrinedecreases expression, increases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-oldecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Acroleinincreases abundance, affects cotreatment, increases oxidation1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Arsenicaffects methylation1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Oils, Volatileincreases abundance, affects cotreatment, affects expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Ribonucleotidesaffects binding1
Seleniumincreases expression1
Smokedecreases expression1
Thiramincreases expression1
Valproic Acidincreases methylation1
Vitamin Eincreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Antirheumatic Agentsincreases expression1
Cadmium Chlorideincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B3FUAbcam HEK293T RBM42 KOTransformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot