RBM41

Summary

RBM41 (RNA binding motif protein 41, HGNC:25617) is a protein-coding gene on chromosome Xq22.3, encoding RNA-binding protein 41 (Q96IZ5). May bind RNA.

Predicted to enable U12 snRNA binding activity and pre-mRNA intronic binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of U12-type spliceosomal complex.

Source: NCBI Gene 55285 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 105 total
• MANE Select transcript: NM_001324242

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25617
Approved symbol	RBM41
Name	RNA binding motif protein 41
Location	Xq22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11016
Ensembl gene	ENSG00000089682
Ensembl biotype	protein_coding
Entrez	55285

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000372479, ENST00000372487, ENST00000434854, ENST00000471079, ENST00000474499, ENST00000475556, ENST00000485676, ENST00000495517, ENST00000685964, ENST00000879623, ENST00000879624, ENST00000914496, ENST00000965479, ENST00000965480, ENST00000965481

RefSeq mRNA: 17 — MANE Select: NM_001324242 NM_001171080, NM_001324242, NM_001324243, NM_001324244, NM_001394116, NM_001394117, NM_001394118, NM_001394119, NM_001394120, NM_001394121, NM_001394122, NM_001394123, NM_001394124, NM_001394125, NM_001394126, NM_001394127, NM_018301

CCDS: CCDS14526, CCDS55472, CCDS94645

Canonical transcript exons

ENST00000685964 — 8 exons

Exon	Start	End
ENSE00000674313	107088436	107088839
ENSE00000866527	107113397	107113468
ENSE00001212903	107069255	107069402
ENSE00003470170	107115352	107115556
ENSE00003533706	107116650	107116766
ENSE00003602049	107115862	107116054
ENSE00003930829	107118766	107118822
ENSE00003936466	107061885	107067693

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 89.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.9759 / max 244.0114, expressed in 1698 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200056	8.8580	1692
200055	0.1179	35

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	89.67	gold quality
cauda epididymis	UBERON:0004360	87.38	gold quality
right uterine tube	UBERON:0001302	86.50	gold quality
jejunal mucosa	UBERON:0000399	86.02	gold quality
sural nerve	UBERON:0015488	85.92	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	85.91	gold quality
diaphragm	UBERON:0001103	85.73	silver quality
colonic epithelium	UBERON:0000397	85.64	gold quality
hair follicle	UBERON:0002073	85.47	gold quality
monocyte	CL:0000576	83.24	gold quality
mononuclear cell	CL:0000842	83.14	gold quality
caput epididymis	UBERON:0004358	83.00	gold quality
olfactory bulb	UBERON:0002264	82.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.77	gold quality
corpus epididymis	UBERON:0004359	82.75	gold quality
leukocyte	CL:0000738	82.59	gold quality
tendon	UBERON:0000043	82.42	gold quality
biceps brachii	UBERON:0001507	81.97	gold quality
buccal mucosa cell	CL:0002336	81.87	silver quality
cortical plate	UBERON:0005343	81.69	gold quality
rectum	UBERON:0001052	81.51	gold quality
mucosa of paranasal sinus	UBERON:0005030	80.96	gold quality
type B pancreatic cell	CL:0000169	80.94	gold quality
gastrocnemius	UBERON:0001388	80.93	gold quality
smooth muscle tissue	UBERON:0001135	80.77	gold quality
bone marrow cell	CL:0002092	80.51	gold quality
muscle of leg	UBERON:0001383	80.47	gold quality
ventricular zone	UBERON:0003053	80.34	gold quality
ganglionic eminence	UBERON:0004023	80.25	gold quality
left lobe of thyroid gland	UBERON:0001120	80.10	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.89
E-GEOD-109979	no	399.96
E-GEOD-99795	no	103.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

270 targeting RBM41, 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-126-5P	100.00	72.71	3180
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbm41	ENSDARG00000054096
mus_musculus	Rbm41	ENSMUSG00000031433
rattus_norvegicus	Rbm41	ENSRNOG00000057622
drosophila_melanogaster	CG44249	FBGN0265184

Paralogs (1): RNPC3 (ENSG00000185946)

Protein

Protein identifiers

RNA-binding protein 41 — Q96IZ5 (reviewed: Q96IZ5)

Alternative names: RNA-binding motif protein 41

All UniProt accessions (3): Q96IZ5, A0A8I5KYC8, H0Y6F9

UniProt curated annotations — full annotation on UniProt →

Function. May bind RNA.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96IZ5-1	1	yes
Q96IZ5-2	2
Q96IZ5-3	3

RefSeq proteins (17): NP_001164551, NP_001311171, NP_001311172, NP_001311173, NP_001381045, NP_001381046, NP_001381047, NP_001381048, NP_001381049, NP_001381050, NP_001381051, NP_001381052, NP_001381053, NP_001381054, NP_001381055, NP_001381056, NP_060771 (=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
IPR045164	RBM41/RNPC3	Family

Pfam: PF00076

UniProt features (21 total): strand 7, splice variant 4, helix 3, chain 1, domain 1, sequence conflict 1, region of interest 1, compositionally biased region 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2CPX	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96IZ5-F1	72.01	0.25

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 (1): 232

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, WANG_RECURRENT_LIVER_CANCER_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_RNA_SPLICING, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_SNRNA_BINDING, GOMF_PRE_MRNA_BINDING, GOCC_U12_TYPE_SPLICEOSOMAL_COMPLEX, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, chrXq22, SNACANNNYSYAGA_UNKNOWN, DELACROIX_RAR_BOUND_ES

GO Biological Process (1): mRNA splicing, via spliceosome (GO:0000398)

GO Molecular Function (5): U12 snRNA binding (GO:0030626), pre-mRNA intronic binding (GO:0097157), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (1): U12-type spliceosomal complex (GO:0005689)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
snRNA binding	1
pre-mRNA binding	1
nucleic acid binding	1
spliceosomal complex	1

Protein interactions and networks

STRING

1827 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM41	RPUSD4	Q96CM3	551
RBM41	NOL6	Q9H6R4	546
RBM41	RBM5	P52756	523
RBM41	NABP1	Q96AH0	523
RBM41	LARP4	Q71RC2	519
RBM41	DDX18	Q9NVP1	496
RBM41	SF3B6	Q9Y3B4	490
RBM41	NT5C3A	Q9H0P0	460
RBM41	A1CF	Q9NQ94	460
RBM41	FAM156A	Q8NDB6	456
RBM41	SRSF9	Q13242	455
RBM41	EIF4E	P06730	454
RBM41	CNOT6L	Q96LI5	454
RBM41	CNOT6	Q9ULM6	447
RBM41	CNOT2	Q9NZN8	439

IntAct

111 interactions, top by confidence:

A	B	Type	Score
RBM41	HNRNPC	psi-mi:“MI:0915”(physical association)	0.740
HNRNPC	RBM41	psi-mi:“MI:0915”(physical association)	0.740
GOLGA2	RBM41	psi-mi:“MI:0915”(physical association)	0.720
RBM41	TRAF2	psi-mi:“MI:0915”(physical association)	0.720
RBM41	RINT1	psi-mi:“MI:0915”(physical association)	0.720
TRAF2	RBM41	psi-mi:“MI:0915”(physical association)	0.720
RINT1	RBM41	psi-mi:“MI:0915”(physical association)	0.720
RBM41	RALYL	psi-mi:“MI:0915”(physical association)	0.670
RALYL	RBM41	psi-mi:“MI:0915”(physical association)	0.670
RBM41	rep	psi-mi:“MI:0915”(physical association)	0.660
TRIM27	RBM41	psi-mi:“MI:0915”(physical association)	0.560
RBM41	MKRN3	psi-mi:“MI:0915”(physical association)	0.560
TRAF1	RBM41	psi-mi:“MI:0915”(physical association)	0.560
KRT40	RBM41	psi-mi:“MI:0915”(physical association)	0.560
RBM41	PNMA1	psi-mi:“MI:0915”(physical association)	0.560
MIPOL1	RBM41	psi-mi:“MI:0915”(physical association)	0.560
RBM41	SPAG5	psi-mi:“MI:0915”(physical association)	0.560
RBM41	LZTS2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (56): RBM41 (Two-hybrid), RBM41 (Two-hybrid), RBM41 (Two-hybrid), RBM41 (Two-hybrid), RBM41 (Two-hybrid), RBM41 (Two-hybrid), RBM41 (Two-hybrid), RBM41 (Two-hybrid), RBM41 (Two-hybrid), TRIM54 (Two-hybrid), RINT1 (Two-hybrid), LZTS2 (Two-hybrid), KRT40 (Two-hybrid), RALYL (Two-hybrid), MIPOL1 (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: F1Q8J0, Q3MHP0, Q3UZ01, Q4G055, Q5R6C7, Q8JZV4, Q8RWV8, Q96IZ5, Q96LT9, A0A0D1DZT6, A1A5R1, A1C646, A1CRM1, A1DGS2, A2Q848, A2R7Z2, A4QNI8, A4RHN3, A6QPR6, A6SGN8, A7EWN6, A7SKE9, A7TQR2, B0XS28, B1WC40, B4KCD5, C1BY64, C8V330, F4JCU0, F4JHI7, O02008, O09032, O22173, O22315, O35698, O43251, O59670, O74968, P08579, P0CR16

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1605 predictions. Top by Δscore:

Variant	Effect	Δscore
X:107115347:CATA:C	donor_loss	1.0000
X:107115348:ATAC:A	donor_loss	1.0000
X:107115349:TAC:T	donor_loss	1.0000
X:107115350:ACCT:A	donor_loss	1.0000
X:107115351:C:CG	donor_loss	1.0000
X:107115393:C:CA	donor_gain	1.0000
X:107115554:CTT:C	acceptor_gain	1.0000
X:107115555:TT:T	acceptor_gain	1.0000
X:107115557:C:CC	acceptor_gain	1.0000
X:107115564:C:CT	acceptor_gain	1.0000
X:107115565:A:T	acceptor_gain	1.0000
X:107115858:TCA:T	donor_loss	1.0000
X:107115859:CA:C	donor_loss	1.0000
X:107115860:A:AC	donor_gain	1.0000
X:107115860:A:T	donor_loss	1.0000
X:107115861:C:CC	donor_gain	1.0000
X:107115861:C:T	donor_loss	1.0000
X:107116050:TACAT:T	acceptor_gain	1.0000
X:107116051:ACAT:A	acceptor_gain	1.0000
X:107116052:CAT:C	acceptor_gain	1.0000
X:107116052:CATC:C	acceptor_gain	1.0000
X:107116054:TC:T	acceptor_loss	1.0000
X:107116055:C:CC	acceptor_gain	1.0000
X:107116055:C:G	acceptor_loss	1.0000
X:107116063:CA:C	acceptor_gain	1.0000
X:107116064:A:AC	acceptor_gain	1.0000
X:107116064:A:C	acceptor_gain	1.0000
X:107116645:CCTA:C	donor_gain	1.0000
X:107116648:A:AC	donor_gain	1.0000
X:107116648:ACT:A	donor_gain	1.0000

AlphaMissense

2893 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:107115911:A:G	L90P	0.997
X:107116698:A:G	L26P	0.996
X:107069273:C:G	A353P	0.995
X:107069392:A:G	L313P	0.994
X:107116686:A:G	L30P	0.994
X:107069268:A:C	F354L	0.993
X:107069268:A:T	F354L	0.993
X:107069270:A:G	F354L	0.993
X:107115964:G:C	F72L	0.993
X:107115964:G:T	F72L	0.993
X:107115965:A:G	F72S	0.993
X:107115966:A:G	F72L	0.993
X:107067654:C:T	G372E	0.992
X:107069398:A:G	L311S	0.992
X:107116689:A:G	L29P	0.992
X:107067617:A:C	F384L	0.991
X:107067617:A:T	F384L	0.991
X:107067619:A:G	F384L	0.991
X:107116030:A:C	F50L	0.991
X:107116030:A:T	F50L	0.991
X:107116032:A:G	F50L	0.991
X:107116674:A:G	L34P	0.991
X:107069356:A:G	L325P	0.990
X:107069388:C:A	K314N	0.986
X:107069388:C:G	K314N	0.986
X:107088466:A:C	F299L	0.986
X:107088466:A:T	F299L	0.986
X:107088468:A:G	F299L	0.986
X:107067673:C:G	A366P	0.984
X:107069272:G:T	A353D	0.984

dbSNP variants (sampled 300 via entrez): RS1000066288 (X:107097929 A>T), RS1000100556 (X:107109798 T>C), RS1000202901 (X:107119669 T>TTA), RS1000224753 (X:107119643 C>T), RS1000239958 (X:107108881 G>C), RS1000253802 (X:107120296 C>A), RS1000255690 (X:107119153 C>T), RS1000269415 (X:107052649 G>A,T), RS1000296036 (X:107088035 A>G), RS1000374245 (X:107083560 T>C), RS1000445715 (X:107062284 G>A), RS1000471365 (X:107108154 T>C), RS1000476518 (X:107062002 A>G), RS1000528293 (X:107109260 A>G), RS1000673461 (X:107080587 G>A,C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
perfluorooctane sulfonic acid	decreases expression	2
Valproic Acid	affects expression, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
perfluorooctanoic acid	decreases expression	1
1-hydroxypyrene	affects cotreatment, decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
perfluorohexanesulfonic acid	decreases expression	1
eprenetapopt	affects expression, affects reaction	1
Benzo(a)pyrene	increases methylation	1
Coumestrol	decreases expression	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ribonucleotides	affects binding	1
Tobacco Smoke Pollution	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Aflatoxin B1	decreases methylation	1
Metals, Heavy	affects cotreatment, decreases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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