RBMS2

Summary

RBMS2 (RNA binding motif single stranded interacting protein 2, HGNC:9909) is a protein-coding gene on chromosome 12q13.3, encoding RNA-binding motif, single-stranded-interacting protein 2 (Q15434).

The protein encoded by this gene is a member of a small family of proteins which bind single stranded DNA/RNA. These proteins are characterized by the presence of two sets of ribonucleoprotein consensus sequence (RNP-CS) that contain conserved motifs, RNP1 and RNP2, originally described in RNA binding proteins, and required for DNA binding. The RBMS proteins have been implicated in such diverse functions as DNA replication, gene transcription, cell cycle progression and apoptosis. This protein was isolated by phenotypic complementation of cdc2 and cdc13 mutants of yeast and is thought to suppress cdc2 and cdc13 mutants through the induction of translation of cdc2.

Source: NCBI Gene 5939 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_002898

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9909
Approved symbol	RBMS2
Name	RNA binding motif single stranded interacting protein 2
Location	12q13.3
Locus type	gene with protein product
Status	Approved
Aliases	SCR3
Ensembl gene	ENSG00000076067
Ensembl biotype	protein_coding
OMIM	602387
Entrez	5939

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 protein_coding, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000262031, ENST00000542360, ENST00000549945, ENST00000550726, ENST00000551369, ENST00000552228, ENST00000552247, ENST00000552916, ENST00000855893, ENST00000855894, ENST00000855895, ENST00000855896, ENST00000855897

RefSeq mRNA: 4 — MANE Select: NM_002898 NM_001414459, NM_001414460, NM_001414461, NM_002898

CCDS: CCDS8923

Canonical transcript exons

ENST00000262031 — 14 exons

Exon	Start	End
ENSE00001260979	56589140	56596193
ENSE00001261042	56521820	56522089
ENSE00003436258	56587554	56587664
ENSE00003466620	56588294	56588374
ENSE00003562543	56581184	56581263
ENSE00003569718	56562417	56562583
ENSE00003586927	56588932	56589018
ENSE00003588523	56586849	56586926
ENSE00003590342	56568975	56569033
ENSE00003616375	56581399	56581508
ENSE00003630255	56571698	56571855
ENSE00003647820	56569899	56569990
ENSE00003691541	56581833	56581879
ENSE00003694618	56582059	56582152

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 95.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.1551 / max 266.2851, expressed in 1699 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126117	12.7119	1688
126120	1.7441	877
126118	0.8149	509
126119	0.5512	346
126116	0.3330	138

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	95.78	gold quality
calcaneal tendon	UBERON:0003701	94.50	gold quality
colonic epithelium	UBERON:0000397	94.28	gold quality
right lung	UBERON:0002167	93.86	gold quality
tendon	UBERON:0000043	93.00	gold quality
tendon of biceps brachii	UBERON:0008188	92.81	gold quality
amniotic fluid	UBERON:0000173	92.49	gold quality
upper lobe of left lung	UBERON:0008952	92.31	gold quality
upper lobe of lung	UBERON:0008948	91.97	gold quality
lung	UBERON:0002048	91.17	gold quality
stromal cell of endometrium	CL:0002255	89.73	gold quality
cardiac muscle of right atrium	UBERON:0003379	88.69	silver quality
omental fat pad	UBERON:0010414	88.13	gold quality
peritoneum	UBERON:0002358	88.10	gold quality
adipose tissue of abdominal region	UBERON:0007808	88.05	gold quality
lower lobe of lung	UBERON:0008949	87.42	gold quality
left lobe of thyroid gland	UBERON:0001120	87.13	gold quality
thyroid gland	UBERON:0002046	87.06	gold quality
subcutaneous adipose tissue	UBERON:0002190	86.95	gold quality
placenta	UBERON:0001987	86.79	gold quality
adipose tissue	UBERON:0001013	86.54	gold quality
right lobe of thyroid gland	UBERON:0001119	86.50	gold quality
left ventricle myocardium	UBERON:0006566	86.18	silver quality
body of uterus	UBERON:0009853	86.03	gold quality
nerve	UBERON:0001021	85.95	gold quality
tibial nerve	UBERON:0001323	85.95	gold quality
ascending aorta	UBERON:0001496	85.67	gold quality
uterine cervix	UBERON:0000002	85.59	gold quality
pancreatic ductal cell	CL:0002079	85.56	gold quality
thoracic aorta	UBERON:0001515	85.56	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.82
E-MTAB-9067	yes	6.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

278 targeting RBMS2, 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-3120-5P	100.00	65.56	965
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-12136	99.98	72.81	5713
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788

Literature-anchored findings (GeneRIF, showing 1)

• RBMS2 acts as a tumor suppressor in breast cancer and positively regulated the expression of P21 by stabilizing its mRNA. (PMID:30514345)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbms2a	ENSDARG00000044179
danio_rerio	rbms2b	ENSDARG00000056150
mus_musculus	Rbms2	ENSMUSG00000040043
rattus_norvegicus	Rbms2	ENSRNOG00000003076

Paralogs (24): ELAVL1 (ENSG00000066044), PABPC1 (ENSG00000070756), PABPC4 (ENSG00000090621), PABPC1L (ENSG00000101104), ELAVL2 (ENSG00000107105), RBM24 (ENSG00000112183), TARDBP (ENSG00000120948), HNRNPR (ENSG00000125944), RBM38 (ENSG00000132819), SYNCRIP (ENSG00000135316), SF3B4 (ENSG00000143368), RBMS3 (ENSG00000144642), PABPC3 (ENSG00000151846), RBMS1 (ENSG00000153250), RBM45 (ENSG00000155636), ELAVL4 (ENSG00000162374), PABPC5 (ENSG00000174740), PUF60 (ENSG00000179950), PABPC1L2B (ENSG00000184388), PABPC1L2A (ENSG00000186288), RBM34 (ENSG00000188739), ELAVL3 (ENSG00000196361), RBM14 (ENSG00000239306), PABPC4L (ENSG00000254535)

Protein

Protein identifiers

RNA-binding motif, single-stranded-interacting protein 2 — Q15434 (reviewed: Q15434)

Alternative names: Suppressor of CDC2 with RNA-binding motif 3

All UniProt accessions (6): Q15434, F5H5C8, F8VQS9, F8VV01, F8VZR4, F8W1T6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (4): NP_001401388, NP_001401389, NP_001401390, NP_002889* (*=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

Pfam: PF00076

UniProt features (18 total): strand 5, modified residue 5, domain 2, helix 2, chain 1, turn 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
1X4E	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15434-F1	63.80	0.33

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 (5): 1, 106, 269, 280, 285

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 209 (showing top): CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, WWTAAGGC_UNKNOWN, GOZGIT_ESR1_TARGETS_DN, CREBP1_Q2, GGGTGGRR_PAX4_03, RODRIGUES_NTN1_TARGETS_DN, CREB_Q4, BLALOCK_ALZHEIMERS_DISEASE_UP, E4F1_Q6, HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP, IRF_Q6, NADLER_OBESITY_DN, GATA2_01, RYTTCCTG_ETS2_B, ELK1_01

GO Biological Process (1): RNA processing (GO:0006396)

GO Molecular Function (5): RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), poly(A) binding (GO:0008143), poly(U) RNA binding (GO:0008266), nucleic acid binding (GO:0003676)

GO Cellular Component (3): nucleus (GO:0005634), cytosol (GO:0005829), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
nucleic acid binding	1
mRNA binding	1
poly-purine tract binding	1
poly-pyrimidine tract binding	1
binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
cellular anatomical structure	1
protein-containing complex	1

Protein interactions and networks

STRING

860 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBMS2	CFHR3	Q02985	808
RBMS2	CFH	P08603	716
RBMS2	CFHR1	Q03591	691
RBMS2	CFHR2	P36980	685
RBMS2	C3	P01024	655
RBMS2	CFHR5	Q9BXR6	646
RBMS2	CFHR4	Q92496	622
RBMS2	C4A	P01028	621
RBMS2	C4A	P01028	589
RBMS2	CD55	P08174	576
RBMS2	GNL3L	Q9NVN8	542
RBMS2	CD46	P15529	506
RBMS2	RRP15	Q9Y3B9	447
RBMS2	PDCD6	O75340	436
RBMS2	SPOP	O43791	435

IntAct

47 interactions, top by confidence:

A	B	Type	Score
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
MRPL2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
AGO1	AIP	psi-mi:“MI:0914”(association)	0.530
GSPT2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
ELAVL2	CASC3	psi-mi:“MI:0914”(association)	0.530
CFTR	CNOT1	psi-mi:“MI:0914”(association)	0.480
RBMS2	SRPK1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
RBMS2	E6	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
E4	MCRIP1	psi-mi:“MI:0914”(association)	0.350
BVLF1	VWA8	psi-mi:“MI:0914”(association)	0.350
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
RBFOX2	PRMT5	psi-mi:“MI:0914”(association)	0.350
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
ENG	IGKV2-28	psi-mi:“MI:0914”(association)	0.350
ORF4a	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
SLC16A11	PABPC4	psi-mi:“MI:0914”(association)	0.350
MYC	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
PRR3	ZNF316	psi-mi:“MI:0914”(association)	0.350
PABPC5	APOBEC3DE	psi-mi:“MI:0914”(association)	0.350
NUP42		psi-mi:“MI:0914”(association)	0.350
LARP4B	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
RBMS2	ZNF275	psi-mi:“MI:0914”(association)	0.350
CAMK2A	SMCHD1	psi-mi:“MI:0914”(association)	0.350
PRR3	RBM47	psi-mi:“MI:0914”(association)	0.350
ZNF346	POTEF	psi-mi:“MI:0914”(association)	0.350
H1-1		psi-mi:“MI:0914”(association)	0.350
RBMS2		psi-mi:“MI:0914”(association)	0.350
APOBEC3DE	AIP	psi-mi:“MI:0914”(association)	0.350
IL17B	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350

BioGRID (277): RBMS2 (Affinity Capture-RNA), RBMS2 (Affinity Capture-RNA), RBMS2 (Affinity Capture-RNA), RBMS2 (Affinity Capture-MS), RBMS2 (Affinity Capture-MS), RBMS2 (Affinity Capture-MS), RBMS2 (Affinity Capture-MS), RBMS2 (Two-hybrid), RBMS2 (Affinity Capture-MS), RBMS2 (Protein-RNA), RBMS2 (Protein-RNA), RBMS2 (Protein-RNA), RBMS2 (Protein-RNA), RBMS2 (Protein-RNA), RBMS2 (Protein-RNA)

ESM2 similar proteins: A0A0R4IEW8, A0JM51, A4QNI8, O09032, O57406, P26378, P29558, Q08E07, Q0V9L3, Q14576, Q15434, Q1RMJ7, Q28GD4, Q3ZBP3, Q3ZC34, Q4R535, Q5NVC8, Q5PQP1, Q5R995, Q5RBD3, Q5SZQ8, Q60899, Q60900, Q61701, Q62176, Q6DGV1, Q6DIV4, Q6XE24, Q6YZW2, Q7SZT7, Q7T3I7, Q7TN33, Q7TSY6, Q7ZWM3, Q8BWL5, Q8CH84, Q8CIN6, Q8N6W0, Q8VC70, Q8VXZ9

Diamond homologs: A0A0R4IEW8, A4QNI8, A8NS61, A8WLV5, B3M3R5, B3NGA1, B4HUE4, B4IX08, B4KX02, B4LFQ9, B4MM23, B4PIS2, B4QRJ0, B5DF91, B8BCZ8, O01671, O04425, O09032, O17310, O61374, O75821, O89086, O97018, P16914, P19339, P19683, P23241, P26378, P28644, P29558, P49310, P60824, P60825, P60826, P70372, P98179, Q04836, Q12926, Q14011, Q14498

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2841 predictions. Top by Δscore:

Variant	Effect	Δscore
12:56522086:GAAG:G	donor_gain	1.0000
12:56522087:AAG:A	donor_loss	1.0000
12:56522088:AG:A	donor_loss	1.0000
12:56522090:G:A	donor_loss	1.0000
12:56562416:GCCAT:G	acceptor_gain	1.0000
12:56562581:GCC:G	donor_gain	1.0000
12:56562584:G:GG	donor_gain	1.0000
12:56569897:A:AG	acceptor_gain	1.0000
12:56569898:G:GG	acceptor_gain	1.0000
12:56569898:GGCT:G	acceptor_gain	1.0000
12:56569991:G:GC	donor_loss	1.0000
12:56569991:G:GG	donor_gain	1.0000
12:56571696:A:AG	acceptor_gain	1.0000
12:56571697:G:GA	acceptor_gain	1.0000
12:56571697:G:T	acceptor_loss	1.0000
12:56571697:GC:G	acceptor_gain	1.0000
12:56571697:GCA:G	acceptor_gain	1.0000
12:56571697:GCAA:G	acceptor_gain	1.0000
12:56571697:GCAAC:G	acceptor_gain	1.0000
12:56572885:A:G	donor_gain	1.0000
12:56581065:T:TA	donor_gain	1.0000
12:56581066:A:AA	donor_gain	1.0000
12:56586847:A:AG	acceptor_gain	1.0000
12:56586848:G:GG	acceptor_gain	1.0000
12:56586848:GA:G	acceptor_gain	1.0000
12:56588292:A:AG	acceptor_gain	1.0000
12:56588293:G:GA	acceptor_gain	1.0000
12:56588293:GT:G	acceptor_gain	1.0000
12:56588293:GTA:G	acceptor_gain	1.0000
12:56588293:GTAT:G	acceptor_gain	1.0000

AlphaMissense

2659 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:56562510:A:C	S54R	1.000
12:56562512:C:A	S54R	1.000
12:56562512:C:G	S54R	1.000
12:56562517:C:T	T56I	1.000
12:56562519:A:C	N57H	1.000
12:56562519:A:G	N57D	1.000
12:56562520:A:T	N57I	1.000
12:56562521:C:A	N57K	1.000
12:56562521:C:G	N57K	1.000
12:56562523:T:A	L58Q	1.000
12:56562523:T:C	L58P	1.000
12:56562525:T:A	Y59N	1.000
12:56562525:T:C	Y59H	1.000
12:56562525:T:G	Y59D	1.000
12:56562526:A:G	Y59C	1.000
12:56562529:T:A	I60N	1.000
12:56562529:T:C	I60T	1.000
12:56562529:T:G	I60S	1.000
12:56562538:T:C	L63S	1.000
12:56562565:T:A	L72H	1.000
12:56562565:T:C	L72P	1.000
12:56562574:T:C	L75P	1.000
12:56562576:T:C	C76R	1.000
12:56562577:G:A	C76Y	1.000
12:56562578:T:G	C76W	1.000
12:56568979:G:C	G80R	1.000
12:56568980:G:A	G80D	1.000
12:56568980:G:T	G80V	1.000
12:56568986:T:A	I82N	1.000
12:56568986:T:G	I82S	1.000

dbSNP variants (sampled 300 via entrez): RS1000021585 (12:56588463 T>A), RS1000022959 (12:56544726 A>G), RS1000062984 (12:56541255 G>T), RS1000073017 (12:56538190 G>A,C), RS1000122355 (12:56571306 A>G), RS1000131362 (12:56594704 C>A,T), RS1000170328 (12:56566067 A>T), RS1000206055 (12:56531288 A>G), RS1000265207 (12:56566496 C>G), RS1000319896 (12:56558723 G>C), RS1000331694 (12:56544442 T>C), RS1000367862 (12:56534920 C>T), RS1000376278 (12:56528816 A>G,T), RS1000407506 (12:56528576 A>T), RS1000476308 (12:56588166 G>A)

Disease associations

OMIM: gene MIM:602387 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST005991_30	Platelet count	4.000000e-09
GCST006249_86	Serum metabolite levels	3.000000e-13
GCST007382_11	Plasma free amino acid levels (adjusted for twenty other PFAAs)	4.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004309	platelet count
EFO:0005134	amino acid measurement
EFO:0009768	glutamine 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
sodium arsenite	decreases expression, increases abundance	2
Valproic Acid	increases expression	2
Cadmium Chloride	decreases expression, increases abundance	2
aristolochic acid I	increases expression	1
bisphenol A	affects expression	1
glycidyl methacrylate	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
cobaltous chloride	decreases expression	1
aflatoxin B2	increases methylation	1
diallyl trisulfide	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Arsenic	decreases expression, increases abundance	1
Cadmium	decreases expression, increases abundance	1
Caffeine	increases phosphorylation	1
Carbamazepine	affects expression	1
Cisplatin	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Quercetin	decreases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Dronabinol	increases expression	1
Vanadates	increases expression	1
Cyclosporine	increases expression	1
Particulate Matter	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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