RBMXL3

Summary

RBMXL3 (RBMX like 3, HGNC:26859) is a protein-coding gene on chromosome Xq23, encoding RNA-binding motif protein, X-linked-like-3 (Q8N7X1). RNA-binding protein involved in glucocorticoid regulation of pulmonary surfactant protein B (SFTPB) mRNA stability.

Predicted to enable mRNA binding activity and snRNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome.

Source: NCBI Gene 139804 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001145346

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26859
Approved symbol	RBMXL3
Name	RBMX like 3
Location	Xq23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40249
Ensembl gene	ENSG00000175718
Ensembl biotype	protein_coding
OMIM	301136
Entrez	139804

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000424776

RefSeq mRNA: 1 — MANE Select: NM_001145346 NM_001145346

CCDS: CCDS55478

Canonical transcript exons

ENST00000424776 — 1 exons

Exon	Start	End
ENSE00001785091	115189410	115192868

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 73.36.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	73.36	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.58	gold quality
right testis	UBERON:0004534	58.31	gold quality
testis	UBERON:0000473	56.61	gold quality
left testis	UBERON:0004533	56.03	gold quality
colonic epithelium	UBERON:0000397	41.25	gold quality
bone marrow cell	CL:0002092	38.01	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
skeletal muscle tissue	UBERON:0001134	36.04	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
sural nerve	UBERON:0015488	35.15	gold quality
tonsil	UBERON:0002372	34.31	gold quality
muscle tissue	UBERON:0002385	33.01	gold quality
bone marrow	UBERON:0002371	32.69	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
urinary bladder	UBERON:0001255	31.00	gold quality
liver	UBERON:0002107	30.49	gold quality
adrenal tissue	UBERON:0018303	30.41	gold quality
descending thoracic aorta	UBERON:0002345	29.88	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.66	gold quality
lymph node	UBERON:0000029	28.74	gold quality
monocyte	CL:0000576	28.63	gold quality
leukocyte	CL:0000738	28.54	gold quality
uterine cervix	UBERON:0000002	28.38	gold quality
calcaneal tendon	UBERON:0003701	28.33	gold quality
cortex of kidney	UBERON:0001225	28.29	gold quality
duodenum	UBERON:0002114	28.14	gold quality
myometrium	UBERON:0001296	28.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting RBMXL3, 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-302C-5P	99.97	72.56	3642
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-548AI	99.69	69.24	1494
HSA-MIR-548BA	99.69	69.14	1514
HSA-MIR-570-5P	99.69	69.24	1494
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-3923	99.52	69.21	446
HSA-MIR-653-5P	99.46	67.35	1300
HSA-MIR-4735-5P	99.43	68.49	1780
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-4773	98.35	67.30	1710
HSA-MIR-376C-3P	97.63	68.88	1263
HSA-MIR-6773-5P	97.04	64.30	595
HSA-MIR-3189-3P	96.80	66.34	896
HSA-MIR-6724-5P	96.41	63.11	507
HSA-MIR-4683	95.29	65.98	631
HSA-MIR-554	95.20	66.98	341
HSA-MIR-1229-5P	94.57	65.78	487

Literature-anchored findings (GeneRIF, showing 1)

• A primate-specific RNA-binding protein (RBMXL3) is involved in glucocorticoid regulation of human pulmonary surfactant protein B (SP-B) mRNA stability. (PMID:33719563)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rbmxl2	ENSMUSG00000073894
rattus_norvegicus	Rbmxl2	ENSRNOG00000090098

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), HNRNPA0 (ENSG00000177733), TRNAU1AP (ENSG00000180098), HNRNPAB (ENSG00000197451), RBMXL1 (ENSG00000213516), HNRNPA1L3 (ENSG00000224578), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

RNA-binding motif protein, X-linked-like-3 — Q8N7X1 (reviewed: Q8N7X1)

All UniProt accessions (1): Q8N7X1

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein involved in glucocorticoid regulation of pulmonary surfactant protein B (SFTPB) mRNA stability.

RefSeq proteins (1): NP_001138818* (*=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
IPR050441	RBM	Family

Pfam: PF00076

UniProt features (30 total): compositionally biased region 15, sequence conflict 9, region of interest 4, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7X1-F1	40.87	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): GOBP_RNA_SPLICING, GOMF_MRNA_BINDING, GOMF_SNRNA_BINDING, chrXq23, GOBP_MRNA_PROCESSING, MAFG_TARGET_GENES, MIR4422, MIR548BA, MIR548AI_MIR570_5P, MIR548AG, MIR4683, MIR6773_5P, MIR1229_5P, MIR6724_5P, GOBP_MRNA_METABOLIC_PROCESS

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

GO Molecular Function (4): RNA binding (GO:0003723), mRNA binding (GO:0003729), snRNA binding (GO:0017069), nucleic acid binding (GO:0003676)

GO Cellular Component (1): organelle (GO:0043226)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA binding	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
nucleic acid binding	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1514 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBMXL3	HNRNPC	P07910	497
RBMXL3	KHDRBS1	Q07666	414
RBMXL3	TEKTL1	Q8IYK2	383
RBMXL3	LRRIQ4	A6NIV6	362
RBMXL3	YTHDC2	Q9H6S0	355
RBMXL3	FRG1	Q14331	355
RBMXL3	WTAP	Q15007	344
RBMXL3	YTHDC1	Q96MU7	344
RBMXL3	METTL16	Q86W50	337
RBMXL3	ALKBH1	Q13686	325
RBMXL3	ETV3L	Q6ZN32	316
RBMXL3	MAGEB16	A2A368	311
RBMXL3	ALKBH5	Q6P6C2	309
RBMXL3	YTHDF1	Q9BYJ9	307
RBMXL3	METTL14	Q9HCE5	304

IntAct

4 interactions, top by confidence:

A	B	Type	Score
N	HNRNPDL	psi-mi:“MI:0914”(association)	0.530
M		psi-mi:“MI:0914”(association)	0.350
KRAS	IGKV2D-29	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): RBMXL3 (Affinity Capture-MS), RBMXL3 (Proximity Label-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Affinity Capture-MS), RBMXL3 (Protein-RNA), RBMXL3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YWL9, A0A0J9YY54, A0A0U1RQI7, A0A494C071, A6NNC1, A6QL64, B3KS81, D3YZV8, E2RYF7, E9Q6E9, F1LWT0, F8W0I5, O60732, P0C8Z4, P0DKJ7, P0DKJ8, P0DKL2, P0DPF3, P18751, P20930, P43537, P53353, P59797, P62521, Q01456, Q08AG5, Q12816, Q3BBV2, Q5H9R4, Q5HY64, Q5JPF3, Q6P902, Q6ZQX7, Q86T75, Q86VE3, Q86VQ3, Q8BGJ3, Q8N307, Q8N7U7, Q8N7X1

Diamond homologs: A0A0A0LLY1, A0A0D1C8Z4, A5A6M3, C0HFE5, D3Z4I3, D4AE41, M0R7T6, O22703, O35698, O75526, O89086, O93235, P04147, P0C8Z4, P10979, P19682, P19683, P19684, P28644, P38159, P39697, P48809, P49310, P49311, P49313, P49314, P60824, P60825, P60826, P84586, P98179, Q03250, Q03251, Q03878, Q04836, Q05966, Q08473, Q08935, Q08937, Q14011

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

131 predictions. Top by Δscore:

Variant	Effect	Δscore
X:115189413:T:TA	donor_gain	0.9800
X:115190449:G:A	donor_gain	0.9000
X:115189486:CA:C	donor_gain	0.8900
X:115189487:AA:A	donor_gain	0.8900
X:115189485:TCA:T	donor_gain	0.8300
X:115189654:C:T	donor_gain	0.8000
X:115190146:AGG:A	donor_gain	0.7300
X:115190146:AGGC:A	donor_gain	0.7200
X:115189491:TCAAA:T	donor_gain	0.7000
X:115190456:G:A	donor_gain	0.6800
X:115189422:C:T	donor_gain	0.6200
X:115189584:C:CA	acceptor_gain	0.6000
X:115190254:C:CT	donor_gain	0.5700
X:115190255:T:TT	donor_gain	0.5700
X:115189427:A:T	donor_gain	0.5600
X:115189423:C:T	donor_gain	0.5500
X:115189419:G:T	donor_gain	0.5200
X:115189426:CA:C	donor_gain	0.5100
X:115190527:G:A	donor_gain	0.5100
X:115189554:T:TA	donor_gain	0.5000
X:115192867:T:C	donor_gain	0.5000
X:115190146:AGGCC:A	donor_gain	0.4800
X:115189851:TCG:T	donor_gain	0.4700
X:115189488:A:C	donor_gain	0.4600
X:115189414:C:A	donor_gain	0.4500
X:115190200:C:A	donor_gain	0.4400
X:115190342:C:CT	donor_gain	0.4400
X:115189957:CAG:C	donor_gain	0.4200
X:115189656:A:AC	donor_gain	0.4100
X:115189419:G:GT	donor_gain	0.3900

AlphaMissense

6954 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:115189592:T:C	F51L	0.998
X:115189594:C:A	F51L	0.998
X:115189594:C:G	F51L	0.998
X:115189602:T:A	V54D	0.998
X:115189607:T:C	F56L	0.998
X:115189609:C:A	F56L	0.998
X:115189609:C:G	F56L	0.998
X:115189608:T:C	F56S	0.997
X:115189598:T:C	F53L	0.996
X:115189600:C:A	F53L	0.996
X:115189600:C:G	F53L	0.996
X:115189472:T:C	F11L	0.995
X:115189474:C:A	F11L	0.995
X:115189474:C:G	F11L	0.995
X:115189523:T:C	F28L	0.995
X:115189525:T:A	F28L	0.995
X:115189525:T:G	F28L	0.995
X:115189593:T:C	F51S	0.995
X:115189473:T:C	F11S	0.994
X:115189524:T:C	F28S	0.994
X:115189635:C:A	A65D	0.993
X:115189512:T:A	L24H	0.992
X:115189596:C:A	A52E	0.992
X:115189599:T:C	F53S	0.991
X:115189608:T:G	F56C	0.991
X:115189470:T:C	L10P	0.990
X:115189476:T:A	I12N	0.989
X:115189512:T:C	L24P	0.989
X:115189485:T:C	L15P	0.988
X:115189634:G:C	A65P	0.988

dbSNP variants (sampled 300 via entrez): RS1000843178 (X:115189944 C>G,T), RS1002469427 (X:115190100 G>A), RS1002926891 (X:115191727 G>A,C,T), RS1005511741 (X:115191115 C>T), RS1005667785 (X:115193157 A>T), RS1005694529 (X:115189194 G>C), RS1005719965 (X:115192689 A>G), RS1007143175 (X:115189909 C>A,G), RS1007583913 (X:115189826 G>C), RS1009145759 (X:115190598 A>C,G), RS1010569231 (X:115192256 C>A,T), RS1010621570 (X:115192094 C>T), RS1011884863 (X:115189403 A>G,T), RS1012325921 (X:115189148 T>A), RS1013300424 (X:115187444 C>A)

Disease associations

OMIM: gene MIM:301136 | 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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
Aflatoxin B1	decreases expression, decreases methylation	2
FR900359	increases phosphorylation	1
2-palmitoylglycerol	increases expression	1
Acetaminophen	decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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