SNRPB

Summary

SNRPB (small nuclear ribonucleoprotein polypeptides B and B1, HGNC:11153) is a protein-coding gene on chromosome 20p13, encoding Small nuclear ribonucleoprotein-associated proteins B and B’ (P14678). Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

The protein encoded by this gene is one of several nuclear proteins that are found in common among U1, U2, U4/U6, and U5 small ribonucleoprotein particles (snRNPs). These snRNPs are involved in pre-mRNA splicing, and the encoded protein may also play a role in pre-mRNA splicing or snRNP structure. Autoantibodies from patients with systemic lupus erythematosus frequently recognize epitopes on the encoded protein. Two transcript variants encoding different isoforms (B and B’) have been found for this gene.

Source: NCBI Gene 6628 — RefSeq curated summary.

At a glance

• Gene–disease (curated): cerebrocostomandibular syndrome (Definitive, GenCC)
• Clinical variants (ClinVar): 168 total — 3 pathogenic, 3 likely-pathogenic
• Phenotypes (HPO): 62
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_003091

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11153
Approved symbol	SNRPB
Name	small nuclear ribonucleoprotein polypeptides B and B1
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	COD, SmB/SmB’, Sm-B/B’, snRNP-B
Ensembl gene	ENSG00000125835
Ensembl biotype	protein_coding
OMIM	182282
Entrez	6628

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 7 protein_coding, 7 retained_intron, 1 nonsense_mediated_decay

ENST00000381342, ENST00000438552, ENST00000474384, ENST00000688423, ENST00000688450, ENST00000688775, ENST00000689440, ENST00000689611, ENST00000690623, ENST00000693393, ENST00000937499, ENST00000937500, ENST00000937501, ENST00000937502, ENST00000963656

RefSeq mRNA: 2 — MANE Select: NM_003091 NM_003091, NM_198216

CCDS: CCDS13026, CCDS13027

Canonical transcript exons

ENST00000381342 — 7 exons

Exon	Start	End
ENSE00000000124	2470688	2470789
ENSE00001388479	2461642	2461939
ENSE00003541235	2463089	2463227
ENSE00003552603	2463747	2463899
ENSE00003680212	2462636	2462761
ENSE00003716068	2465708	2465819
ENSE00003746359	2467607	2467758

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 100.8345 / max 520.5188, expressed in 1825 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186095	95.9606	1825
186094	4.1195	1444
186093	0.7544	402

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endometrium epithelium	UBERON:0004811	98.54	gold quality
granulocyte	CL:0000094	98.43	gold quality
mucosa of transverse colon	UBERON:0004991	98.23	gold quality
esophagus mucosa	UBERON:0002469	98.19	gold quality
skin of leg	UBERON:0001511	98.15	gold quality
skin of abdomen	UBERON:0001416	98.11	gold quality
thymus	UBERON:0002370	98.06	gold quality
lower esophagus mucosa	UBERON:0035834	98.00	gold quality
left uterine tube	UBERON:0001303	97.97	gold quality
pharyngeal mucosa	UBERON:0000355	97.91	gold quality
lymph node	UBERON:0000029	97.88	gold quality
gingival epithelium	UBERON:0001949	97.87	gold quality
ectocervix	UBERON:0012249	97.85	gold quality
spleen	UBERON:0002106	97.79	gold quality
esophagus	UBERON:0001043	97.78	gold quality
type B pancreatic cell	CL:0000169	97.77	gold quality
monocyte	CL:0000576	97.72	gold quality
vermiform appendix	UBERON:0001154	97.71	gold quality
body of uterus	UBERON:0009853	97.71	gold quality
leukocyte	CL:0000738	97.66	gold quality
embryo	UBERON:0000922	97.66	gold quality
ventricular zone	UBERON:0003053	97.66	gold quality
mononuclear cell	CL:0000842	97.64	gold quality
zone of skin	UBERON:0000014	97.64	gold quality
transverse colon	UBERON:0001157	97.55	gold quality
mucosa of stomach	UBERON:0001199	97.50	gold quality
upper lobe of left lung	UBERON:0008952	97.50	gold quality
gingiva	UBERON:0001828	97.49	gold quality
small intestine Peyer’s patch	UBERON:0003454	97.43	gold quality
lower esophagus	UBERON:0013473	97.43	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-MTAB-6819	yes	1073.08
E-MTAB-8142	yes	114.90
E-HCAD-10	yes	39.80
E-HCAD-5	yes	38.98
E-CURD-122	yes	26.01
E-GEOD-125970	yes	25.61
E-HCAD-13	yes	22.63
E-CURD-46	yes	22.32
E-MTAB-9067	yes	21.06
E-MTAB-10553	yes	8.03
E-MTAB-11011	no	475.46
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MEF2A, MYC

miRNA regulators (miRDB)

27 targeting SNRPB, 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-340-5P	100.00	72.50	4437
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-7156-5P	99.64	68.81	1369
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4273	99.45	67.93	1206
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-7114-5P	98.51	67.87	1349
HSA-MIR-2117	98.48	67.97	1307
HSA-MIR-4717-5P	98.19	67.97	894
HSA-MIR-4457	98.09	67.12	1274
HSA-MIR-4759	97.39	65.86	608
HSA-MIR-6895-5P	97.05	64.96	522
HSA-MIR-873-3P	96.84	66.09	786
HSA-MIR-134-3P	96.83	66.22	1001
HSA-MIR-6856-3P	96.47	66.27	781
HSA-MIR-7160-3P	96.40	64.15	462
HSA-MIR-10525-3P	96.32	68.04	699
HSA-MIR-1291	96.28	65.89	1224
HSA-MIR-6888-5P	95.89	63.78	831
HSA-MIR-6805-5P	95.79	64.86	670
HSA-MIR-6775-3P	95.76	65.91	982
HSA-MIR-4512	95.26	63.08	371
HSA-MIR-3672	94.46	65.67	646
HSA-MIR-6864-3P	94.46	65.97	625
HSA-MIR-1296-5P	93.94	67.71	305
HSA-MIR-4681	89.50	61.59	122

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 15)

• Alternative splice form with additional novel exon (2b) found in short-tailed opossum, wallaby and human. (PMID:10556313)
• in addition to affecting coilin-coilin interaction and localization in the nucleus, the phosphorylation state of coilin also impacts its interaction with SMN and SmB’ and may play a role in controlling U snRNP cycling through the Cajal bodies. (PMID:19997741)
• Highly mobile SmB protein-trafficking vesicles in neural cells are dependent on the cellular levels of SMN and SmB for their morphology and mobility. (PMID:24357717)
• Mutations in the regulatory alternative exon of SNRPB disrupted it’s auto-regulation and caused cerebro-costo-mandibular syndrome. (PMID:25047197)
• Cerebro-costo-mandibular syndrome is due to heterozygous mutations in SNRPB. (PMID:25504470)
• These results confirm the specificity of SNRPB mutations in CCMS and provide further evidence for the role of spliceosomal proteins in craniofacial and thoracic development. (PMID:26971886)
• Our study provides new insights into how RBPs, and specifically SNRPB, regulate gene expression and directly impact GBM development. (PMID:27287018)
• The study unveils a novel role of SNRPB in facilitating non-small cell lung cancer tumorigenesis via regulation of RAB26 expression. (PMID:31511502)
• c-Myc-mediated SNRPB upregulation functions as an oncogene in hepatocellular carcinoma. (PMID:31930637)
• SNRPB promotes cervical cancer progression through repressing p53 expression. (PMID:32106364)
• SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma. (PMID:33289700)
• Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation. (PMID:34984976)
• [Regulatory effect of small nuclear ribonucleoprotein-associated protein B on proliferation and metastasis of liver cancer cells]. (PMID:35152671)
• The splicing factor SNRPB promotes ovarian cancer progression through regulating aberrant exon skipping of POLA1 and BRCA2. (PMID:37391593)
• SNRPB promotes the progression of hepatocellular carcinoma via regulating cell cycle, oxidative stress, and ferroptosis. (PMID:38189879)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrpb	ENSDARG00000011125
mus_musculus	Snrpb	ENSMUSG00000027404
rattus_norvegicus	Snrpb	ENSRNOG00000006961
drosophila_melanogaster	SmB	FBGN0262601
caenorhabditis_elegans	snr-2	WBGENE00004915

Paralogs (1): SNRPN (ENSG00000128739)

Protein

Protein identifiers

Small nuclear ribonucleoprotein-associated proteins B and B’ — P14678 (reviewed: P14678)

Alternative names: Sm protein B/B'

All UniProt accessions (3): P14678, Q66K91, S4R3P3

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs. As part of the U7 snRNP it is involved in histone pre-mRNA 3’-end processing.

Subunit / interactions. Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. Component of the U1 snRNP. The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. Component of the U7 snRNP complex, or U7 Sm protein core complex, that is composed of the U7 snRNA and at least LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF and SNRPG; the complex does not contain SNRPD1 and SNRPD2. Component of the minor spliceosome, which splices U12-type introns. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP. Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1. Interacts with TDRD3 and SNUPN. Interacts with PRMT5; interaction leads to its symmetric arginine dimethylation. Interacts with TDRD6; interaction promotes association with PRMT5. Interacts with SMN1; the interaction is direct.

Subcellular location. Cytoplasm. Cytosol. Nucleus.

Post-translational modifications. Methylated by PRMT5. Arg-108 and Arg-112 are dimethylated, probably to asymmetric dimethylarginine (PubMed:16087681, Ref.10).

Disease relevance. Cerebrocostomandibular syndrome (CCMS) [MIM:117650] A syndrome characterized by severe micrognathia, rib defects ranging from a few dorsal rib segments to complete absence of ossification, and intellectual disability. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. Patients with the autoimmune disease systemic lupus erythematosus (SLE) have autoantibodies directed against some of the individual snRNP polypeptides. The most common autoantigen is called Sm. B/b’ bear Sm epitopes.

Similarity. Belongs to the snRNP SmB/SmN family.

Isoforms (3)

UniProt ID	Names	Canonical?
P14678-1	SM-B'	yes
P14678-2	SM-B
P14678-3	SM-B1

RefSeq proteins (2): NP_003082, NP_937859 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR017131	snRNP-assoc_SmB/SmN	Family
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (38 total): modified residue 8, strand 6, repeat 5, sequence variant 5, sequence conflict 3, compositionally biased region 2, splice variant 2, helix 2, region of interest 2, chain 1, domain 1, turn 1

Structure

Experimental structures (PDB)

75 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
1D3B	X-RAY DIFFRACTION	2
7EVO	ELECTRON MICROSCOPY	2.5
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
8HK1	ELECTRON MICROSCOPY	2.7
8C6J	ELECTRON MICROSCOPY	2.8
9NH5	ELECTRON MICROSCOPY	2.82
9NH6	ELECTRON MICROSCOPY	2.82
6ID1	ELECTRON MICROSCOPY	2.86
7DVQ	ELECTRON MICROSCOPY	2.89
6ID0	ELECTRON MICROSCOPY	2.9
6QW6	ELECTRON MICROSCOPY	2.92
6ICZ	ELECTRON MICROSCOPY	3
7VPX	ELECTRON MICROSCOPY	3
8I0R	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
8I0V	ELECTRON MICROSCOPY	3
9GCL	ELECTRON MICROSCOPY	3
7QTT	ELECTRON MICROSCOPY	3.1
8Q91	ELECTRON MICROSCOPY	3.1
9N96	ELECTRON MICROSCOPY	3.18
6V4X	ELECTRON MICROSCOPY	3.2
8H6E	ELECTRON MICROSCOPY	3.2
8Q7Q	ELECTRON MICROSCOPY	3.2
8RC0	ELECTRON MICROSCOPY	3.2
9GC0	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
4PJO	X-RAY DIFFRACTION	3.3
6QDV	ELECTRON MICROSCOPY	3.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P14678-F1	71.41	0.31

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 (8): 108, 108, 108, 112, 112, 112, 147, 172

Function

Pathways and Gene Ontology

Reactome pathways

23 pathways

ID	Pathway
R-HSA-111367	SLBP independent Processing of Histone Pre-mRNAs
R-HSA-191859	snRNP Assembly
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway
R-HSA-73856	RNA Polymerase II Transcription Termination
R-HSA-77588	SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
R-HSA-9754678	SARS-CoV-2 modulates host translation machinery
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-9943411	CHD1 and CHD2 subfamily
R-HSA-1643685	Disease
R-HSA-194441	Metabolism of non-coding RNA
R-HSA-5663205	Infectious disease
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-75067	Processing of Capped Intronless Pre-mRNA
R-HSA-8953854	Metabolism of RNA
R-HSA-9679506	SARS-CoV Infections
R-HSA-9694516	SARS-CoV-2 Infection
R-HSA-9705683	SARS-CoV-2-host interactions
R-HSA-9824446	Viral Infection Pathways

MSigDB gene sets: 445 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP, MODULE_151, ENK_UV_RESPONSE_KERATINOCYTE_UP, MORF_UBE2I, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_RNA_METHYLATION, PATIL_LIVER_CANCER, PUJANA_CHEK2_PCC_NETWORK, BROWNE_HCMV_INFECTION_24HR_UP, MUELLER_PLURINET, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_RNA_MODIFICATION, REACTOME_MRNA_3_END_PROCESSING

GO Biological Process (7): spliceosomal snRNP assembly (GO:0000387), mRNA splicing, via spliceosome (GO:0000398), protein methylation (GO:0006479), RNA splicing (GO:0008380), 7-methylguanosine cap hypermethylation (GO:0036261), U2-type prespliceosome assembly (GO:1903241), mRNA processing (GO:0006397)

GO Molecular Function (7): RNA binding (GO:0003723), telomerase RNA binding (GO:0070034), snRNP binding (GO:0070990), histone pre-mRNA DCP binding (GO:0071208), U1 snRNP binding (GO:1990446), U2 snRNP binding (GO:1990447), protein binding (GO:0005515)

GO Cellular Component (23): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U5 snRNP (GO:0005682), U7 snRNP (GO:0005683), U2-type spliceosomal complex (GO:0005684), U1 snRNP (GO:0005685), U2 snRNP (GO:0005686), U4 snRNP (GO:0005687), U12-type spliceosomal complex (GO:0005689), telomerase holoenzyme complex (GO:0005697), cytoplasm (GO:0005737), cytosol (GO:0005829), small nuclear ribonucleoprotein complex (GO:0030532), methylosome (GO:0034709), SMN-Sm protein complex (GO:0034719), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type prespliceosome (GO:0071004), U2-type precatalytic spliceosome (GO:0071005), U2-type catalytic step 2 spliceosome (GO:0071007), catalytic step 2 spliceosome (GO:0071013), histone pre-mRNA 3’end processing complex (GO:0071204), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
Metabolism of RNA	3
Processing of Capped Intronless Pre-mRNA	2
mRNA Splicing	2
Metabolism of non-coding RNA	1
RNA Polymerase II Transcription	1
SARS-CoV-2-host interactions	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
CHD chromatin remodelers	1
Disease	1
Processing of Capped Intron-Containing Pre-mRNA	1
Gene expression (Transcription)	1
Viral Infection Pathways	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
spliceosomal snRNP complex	4
cellular anatomical structure	3
nuclear protein-containing complex	3
ribonucleoprotein complex	3
cytoplasm	3
U2-type spliceosomal complex	3
U2 snRNP	3
RNA processing	2
RNA binding	2
snRNP binding	2
spliceosomal complex	2
Sm-like protein family complex	2
U1 snRNP	2
mRNA splicing, via spliceosome	1
protein-RNA complex assembly	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
protein alkylation	1
macromolecule methylation	1
RNA methylation	1
RNA capping	1
spliceosomal complex assembly	1
mRNA metabolic process	1
nucleic acid binding	1
ribonucleoprotein complex binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
small nuclear ribonucleoprotein complex	1
catalytic complex	1
intracellular anatomical structure	1
methyltransferase complex	1
SMN complex	1
U5 snRNP	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
prespliceosome	1
U4/U6 x U5 tri-snRNP complex	1
precatalytic spliceosome	1
U6 snRNP	1

Protein interactions and networks

STRING

2783 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNRPB	SNRPE	P08578	998
SNRPB	SNRPD2	P43330	997
SNRPB	SNRPD3	P43331	994
SNRPB	SNRPF	P62306	960
SNRPB	SNRPG	P62308	955
SNRPB	SNRPC	P09234	953
SNRPB	SNRNP70	P08621	908
SNRPB	WBP4	O75554	897
SNRPB	SNRPD1	P13641	871
SNRPB	SNRPB2	P08579	856
SNRPB	GEMIN2	O14893	823
SNRPB	WDR77	Q9BQA1	785
SNRPB	SF3B4	Q15427	775
SNRPB	COIL	P38432	774
SNRPB	SNRPA	P09012	741

IntAct

173 interactions, top by confidence:

A	B	Type	Score
IFIT1	IFIT3	psi-mi:“MI:0914”(association)	0.920
SNRPB	CD2BP2	psi-mi:“MI:0915”(physical association)	0.880
CD2BP2	SNRPB	psi-mi:“MI:0915”(physical association)	0.880
SNRPB	CD2BP2	psi-mi:“MI:0403”(colocalization)	0.880
SNRPB	CD2BP2	psi-mi:“MI:0407”(direct interaction)	0.880
CD2BP2	SNRPB	psi-mi:“MI:0407”(direct interaction)	0.880
SNRPD3	SNRPB	psi-mi:“MI:0915”(physical association)	0.880
MAPK14	RPS6KA4	psi-mi:“MI:0914”(association)	0.870
SMN1	SNRPB	psi-mi:“MI:0914”(association)	0.850
GEMIN4	SNRPB	psi-mi:“MI:0915”(physical association)	0.850
GEMIN4	SNRPB	psi-mi:“MI:0407”(direct interaction)	0.850
SMN1	SNRPB	psi-mi:“MI:0915”(physical association)	0.850
SNRPB	SMN1	psi-mi:“MI:0407”(direct interaction)	0.850
SNRPB	SNRNP70	psi-mi:“MI:0915”(physical association)	0.830
SNRNP70	SNRPB	psi-mi:“MI:0914”(association)	0.830
CLNS1A	PRMT5	psi-mi:“MI:0914”(association)	0.830
IFIT2	IFIT3	psi-mi:“MI:0914”(association)	0.780
CLNS1A	SNRPB	psi-mi:“MI:0914”(association)	0.770
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
CLNS1A	SNRPB	psi-mi:“MI:0915”(physical association)	0.770
YBX1	HNRNPR	psi-mi:“MI:0915”(physical association)	0.770
GEMIN5	SNRPB	psi-mi:“MI:0914”(association)	0.730
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.730
SART3	PRPF4	psi-mi:“MI:0914”(association)	0.730

BioGRID (813): SNRPB (Affinity Capture-MS), SNRPB (Two-hybrid), SNRPB (Two-hybrid), SNRPB (Two-hybrid), SNRPB (Two-hybrid), PNMA1 (Two-hybrid), CALCOCO2 (Two-hybrid), CD2BP2 (Two-hybrid), RBPMS (Two-hybrid), TFIP11 (Two-hybrid), SS18L1 (Two-hybrid), BANP (Two-hybrid), CEP55 (Two-hybrid), L3MBTL3 (Two-hybrid), KRT40 (Two-hybrid)

ESM2 similar proteins: D4A055, O00305, O14639, O70133, P14678, P17136, P17427, P18484, P27048, P30626, P48444, P62314, P62315, P62318, P62320, P62323, P63162, P63163, P63164, Q08211, Q13330, Q16514, Q17QN3, Q28141, Q2HJH9, Q3T174, Q3ZC10, Q4R5F6, Q58DW4, Q5R4U9, Q5R6I0, Q5R874, Q5RA77, Q5XIT1, Q5XJY5, Q60HD3, Q62599, Q66H80, Q6P069, Q6PER3

Diamond homologs: A1CE19, A1DM27, A4FUI2, A4RQ29, A5DRQ6, A6R363, A6S5C9, A7F5M4, A7UXE4, A8MWD9, A8NHT8, B0DWN3, B6YUU5, C5A1H1, C6A1T2, O22823, O26745, O29386, O42978, O59734, O74016, O74499, O74966, P0CR24, P0CR25, P14678, P17136, P27048, P34659, P40089, P40204, P54999, P57670, P57743, P62306, P62307, P62308, P62309, P62310, P62311

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SNRPB	“form complex”	“U4/U6.U5 snRNP complex”	binding
SNRPB	“form complex”	“U2 snRNP complex”	binding
SNRPB	“form complex”	“U1 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 166 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:

Pathway	Partners	Fold	FDR
Metabolism of non-coding RNA	9	44.3×	8e-12
mRNA Splicing - Minor Pathway	14	24.3×	2e-14
mRNA Splicing	27	23.0×	1e-27
Processing of Capped Intron-Containing Pre-mRNA	34	21.6×	2e-34
snRNP Assembly	13	21.3×	2e-12
SARS-CoV-2 modulates host translation machinery	11	19.1×	5e-10
mRNA Splicing - Major Pathway	45	19.1×	1e-43
RNA Polymerase II Transcription Termination	10	17.0×	2e-08

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	17	66.8×	1e-25
spliceosomal tri-snRNP complex assembly	7	53.1×	4e-09
spliceosomal complex assembly	13	52.9×	1e-17
U2-type prespliceosome assembly	11	46.4×	4e-14
mRNA cis splicing, via spliceosome	6	40.2×	5e-07
RNA splicing, via transesterification reactions	7	29.5×	3e-07
mRNA splicing, via spliceosome	46	28.5×	3e-52
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	5	15.8×	8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	3
Uncertain significance	74
Likely benign	60
Benign	18

Top pathogenic / likely-pathogenic (6)

Variant ID	HGVS	Classification
183432	NM_003091.4(SNRPB):c.155+302G>C	Pathogenic
183433	NM_003091.4(SNRPB):c.155+302G>T	Pathogenic
183434	NM_003091.4(SNRPB):c.155+406C>A	Pathogenic
2413043	NM_003091.4(SNRPB):c.621del (p.Gly208fs)	Likely pathogenic
3235903	NM_003091.4(SNRPB):c.267+4dup	Likely pathogenic
981739	NM_003091.4(SNRPB):c.560-1G>T	Likely pathogenic

SpliceAI

1126 predictions. Top by Δscore:

Variant	Effect	Δscore
20:2462631:CTTA:C	donor_loss	1.0000
20:2462632:TTACC:T	donor_loss	1.0000
20:2462634:A:AC	donor_gain	1.0000
20:2462635:C:CC	donor_gain	1.0000
20:2462635:CCT:C	donor_gain	1.0000
20:2462635:CCTCG:C	donor_gain	1.0000
20:2462757:CATGC:C	acceptor_gain	1.0000
20:2462758:ATGC:A	acceptor_gain	1.0000
20:2462758:ATGCC:A	acceptor_loss	1.0000
20:2462759:TGC:T	acceptor_gain	1.0000
20:2462759:TGCCT:T	acceptor_loss	1.0000
20:2462761:CCTG:C	acceptor_loss	1.0000
20:2462762:C:CC	acceptor_gain	1.0000
20:2462762:C:CG	acceptor_loss	1.0000
20:2462763:T:A	acceptor_loss	1.0000
20:2463083:CCTCA:C	donor_loss	1.0000
20:2463084:CTCA:C	donor_loss	1.0000
20:2463085:TCA:T	donor_loss	1.0000
20:2463086:CACCT:C	donor_loss	1.0000
20:2463088:CCTGG:C	donor_loss	1.0000
20:2463223:ATCAC:A	acceptor_gain	1.0000
20:2463224:TCAC:T	acceptor_gain	1.0000
20:2463225:CAC:C	acceptor_gain	1.0000
20:2463225:CACC:C	acceptor_gain	1.0000
20:2463226:AC:A	acceptor_gain	1.0000
20:2463226:ACC:A	acceptor_loss	1.0000
20:2463227:CC:C	acceptor_gain	1.0000
20:2463228:C:CC	acceptor_gain	1.0000
20:2463228:C:T	acceptor_gain	1.0000
20:2463238:A:C	acceptor_gain	1.0000

AlphaMissense

1478 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:2463787:A:T	L127H	1.000
20:2463838:G:T	A110D	1.000
20:2465725:C:G	G84R	1.000
20:2465725:C:T	G84R	1.000
20:2465740:A:G	S79P	1.000
20:2465742:A:T	V78D	1.000
20:2465745:A:G	L77P	1.000
20:2465745:A:T	L77Q	1.000
20:2465754:C:A	G74V	1.000
20:2465754:C:G	G74A	1.000
20:2465754:C:T	G74E	1.000
20:2465755:C:A	G74W	1.000
20:2465755:C:G	G74R	1.000
20:2465755:C:T	G74R	1.000
20:2465757:C:A	R73L	1.000
20:2465760:A:G	L72P	1.000
20:2465763:A:C	L71R	1.000
20:2465763:A:G	L71P	1.000
20:2465763:A:T	L71Q	1.000
20:2465766:A:T	V70E	1.000
20:2465769:A:G	L69P	1.000
20:2465772:C:A	G68V	1.000
20:2465772:C:T	G68D	1.000
20:2465773:C:A	G68C	1.000
20:2465773:C:G	G68R	1.000
20:2465773:C:T	G68S	1.000
20:2465775:A:G	L67P	1.000
20:2465775:A:T	L67H	1.000
20:2465781:C:G	R65P	1.000
20:2467615:T:A	R49S	1.000

dbSNP variants (sampled 300 via entrez): RS1000063087 (20:2466178 G>C), RS1000845624 (20:2469474 C>T), RS1001068628 (20:2462855 A>G,T), RS1001241788 (20:2472228 C>G), RS1001688019 (20:2466298 G>A,C), RS1001736908 (20:2467573 C>T), RS1001815247 (20:2471985 A>G), RS1001870823 (20:2470608 G>T), RS1002032922 (20:2469467 G>A), RS1002038663 (20:2462433 C>T), RS1002070888 (20:2469174 T>C), RS1002118995 (20:2465937 C>G), RS1002718893 (20:2467442 C>G), RS1003463918 (20:2461359 G>C), RS1003496491 (20:2464483 G>A)

Disease associations

OMIM: gene MIM:182282 | disease phenotypes: MIM:117650, MIM:261800

GenCC curated gene-disease

Disease	Classification	Inheritance
cerebrocostomandibular syndrome	Definitive	Autosomal dominant

Mondo (3): cerebrocostomandibular syndrome (MONDO:0007301), intellectual disability (MONDO:0001071), isolated Pierre-Robin syndrome (MONDO:0009869)

Orphanet (3): Cerebrocostomandibular syndrome (Orphanet:1393), Isolated Pierre Robin sequence (Orphanet:718), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

62 total (30 of 62 shown, HPO-id order):

HPO	Term
HP:0000003	Multicystic kidney dysplasia
HP:0000006	Autosomal dominant inheritance
HP:0000085	Horseshoe kidney
HP:0000086	Ectopic kidney
HP:0000107	Renal cyst
HP:0000162	Glossoptosis
HP:0000175	Cleft palate
HP:0000185	Cleft soft palate
HP:0000201	Pierre-Robin sequence
HP:0000218	High palate
HP:0000252	Microcephaly
HP:0000272	Malar flattening
HP:0000286	Epicanthus
HP:0000343	Long philtrum
HP:0000347	Micrognathia
HP:0000358	Posteriorly rotated ears
HP:0000369	Low-set ears
HP:0000405	Conductive hearing impairment
HP:0000413	Atresia of the external auditory canal
HP:0000465	Webbed neck
HP:0000494	Downslanted palpebral fissures
HP:0000670	Carious teeth
HP:0000878	11 pairs of ribs
HP:0001249	Intellectual disability
HP:0001374	Congenital hip dislocation
HP:0001511	Intrauterine growth retardation
HP:0001522	Death in infancy
HP:0001545	Anteriorly placed anus
HP:0001561	Polyhydramnios
HP:0001591	Bell-shaped thorax

GWAS associations

0 associations (top):

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D010855	Pierre Robin Syndrome	C05.500.460.606; C05.660.207.540.460.606; C07.320.440.606; C07.650.500.460.606; C16.131.621.207.540.460.606; C16.131.850.500.460.606
C562538	Cerebrocostomandibular Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725130 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, decreases expression, increases expression	4
Valproic Acid	decreases expression, affects cotreatment, increases expression	3
Particulate Matter	increases expression, decreases expression, increases abundance, affects expression	3
bisphenol F	increases expression, increases methylation	2
Lead	affects expression, decreases expression	2
Tobacco Smoke Pollution	increases expression	2
Tretinoin	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
arsenite	affects binding, decreases reaction	1
cobaltous chloride	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
nickel sulfate	increases expression	1
yessotoxin	decreases expression	1
CGP 52608	increases reaction, affects binding	1
CD 437	decreases expression	1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic acid	decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1
bisphenol AF	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Vehicle Emissions	increases expression	1
Benzo(a)pyrene	increases methylation	1
Calcitriol	decreases expression	1
Cisplatin	increases expression	1
Clozapine	increases expression	1

ChEMBL screening assays

6 unique, capped per target: 6 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5697165	Binding	Inhibition of SNRPB (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — Nature

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476	PHASE2/PHASE3	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796	PHASE1/PHASE2	COMPLETED	Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672	EARLY_PHASE1	RECRUITING	Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948	Not specified	COMPLETED	Healthy Lifestyles for People With Intellectual Disabilities
NCT01087320	Not specified	RECRUITING	Genome Medical Sequencing for Gene Discovery
NCT01652963	Not specified	UNKNOWN	Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395	Not specified	COMPLETED	Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554	Not specified	COMPLETED	Research and Characterization of New Genes Involved in Intellectual Disability
NCT01915381	Not specified	COMPLETED	Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623	Not specified	COMPLETED	Pivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773	Not specified	COMPLETED	Support Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849	Not specified	COMPLETED	Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041	Not specified	COMPLETED	Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438	Not specified	COMPLETED	Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761	Not specified	COMPLETED	Apparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420	Not specified	ACTIVE_NOT_RECRUITING	Mapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459	Not specified	ACTIVE_NOT_RECRUITING	Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081	Not specified	COMPLETED	Development and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502	Not specified	COMPLETED	Enhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277	Not specified	COMPLETED	Diabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754	Not specified	COMPLETED	Weight Management for Adolescents With IDD
NCT02591446	Not specified	COMPLETED	Transcranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868	Not specified	COMPLETED	Evaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394	Not specified	UNKNOWN	FCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614	Not specified	COMPLETED	Psychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405	Not specified	COMPLETED	TMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders