Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10992
Gene name	Splicing factor 3b subunit 2
Gene symbol	SF3B2
Synonyms (NCBI Gene)	CFMCus1HFMSAP145SF3B145SF3b1SF3b150
Chromosome	11
Chromosome location	11q13.1
Summary	This gene encodes subunit 2 of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-m

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1057519959	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1057519960	A>G	Likely-pathogenic	Missense variant, coding sequence variant

Show/Hide all (98)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029398	hsa-miR-26b-5p	Microarray	19088304
MIRT043738	hsa-miR-342-3p	CLASH	23622248
MIRT043563	hsa-miR-331-3p	CLASH	23622248
MIRT043182	hsa-miR-324-5p	CLASH	23622248
MIRT041928	hsa-miR-484	CLASH	23622248
MIRT041282	hsa-miR-193b-3p	CLASH	23622248
MIRT040893	hsa-miR-18a-3p	CLASH	23622248
MIRT039791	hsa-miR-615-3p	CLASH	23622248
MIRT038862	hsa-miR-93-3p	CLASH	23622248
MIRT036927	hsa-miR-877-3p	CLASH	23622248
MIRT731218	hsa-miR-3189-3p	qRT-PCRLuciferase reporter assayWestern blot	25645911
MIRT731218	hsa-miR-3189-3p	qRT-PCRLuciferase reporter assayWestern blot	25645911
MIRT1341236	hsa-miR-1292	CLIP-seq
MIRT1341237	hsa-miR-1296	CLIP-seq
MIRT1341238	hsa-miR-203	CLIP-seq
MIRT1341239	hsa-miR-3124-3p	CLIP-seq
MIRT1341240	hsa-miR-3153	CLIP-seq
MIRT1341241	hsa-miR-3613-3p	CLIP-seq
MIRT1341242	hsa-miR-3926	CLIP-seq
MIRT1341243	hsa-miR-4261	CLIP-seq
MIRT1341244	hsa-miR-4471	CLIP-seq
MIRT1341245	hsa-miR-4512	CLIP-seq
MIRT1341246	hsa-miR-4645-5p	CLIP-seq
MIRT1341247	hsa-miR-4668-5p	CLIP-seq
MIRT1341248	hsa-miR-4673	CLIP-seq
MIRT1341249	hsa-miR-4699-3p	CLIP-seq
MIRT1341250	hsa-miR-4734	CLIP-seq
MIRT1341251	hsa-miR-502-5p	CLIP-seq
MIRT1341252	hsa-miR-520d-5p	CLIP-seq
MIRT1341253	hsa-miR-524-5p	CLIP-seq
MIRT1341254	hsa-miR-578	CLIP-seq
MIRT1341255	hsa-miR-581	CLIP-seq
MIRT1341256	hsa-miR-648	CLIP-seq
MIRT1341257	hsa-miR-876-3p	CLIP-seq
MIRT1341238	hsa-miR-203	CLIP-seq
MIRT1341239	hsa-miR-3124-3p	CLIP-seq
MIRT1341240	hsa-miR-3153	CLIP-seq
MIRT1341243	hsa-miR-4261	CLIP-seq
MIRT2100992	hsa-miR-4511	CLIP-seq
MIRT1341247	hsa-miR-4668-5p	CLIP-seq
MIRT1341249	hsa-miR-4699-3p	CLIP-seq
MIRT1341251	hsa-miR-502-5p	CLIP-seq
MIRT1341252	hsa-miR-520d-5p	CLIP-seq
MIRT1341253	hsa-miR-524-5p	CLIP-seq
MIRT2100993	hsa-miR-548b-3p	CLIP-seq
MIRT1341236	hsa-miR-1292	CLIP-seq
MIRT1341237	hsa-miR-1296	CLIP-seq
MIRT2325504	hsa-miR-147	CLIP-seq
MIRT1341239	hsa-miR-3124-3p	CLIP-seq
MIRT1341240	hsa-miR-3153	CLIP-seq
MIRT1341241	hsa-miR-3613-3p	CLIP-seq
MIRT1341242	hsa-miR-3926	CLIP-seq
MIRT1341243	hsa-miR-4261	CLIP-seq
MIRT1341244	hsa-miR-4471	CLIP-seq
MIRT1341245	hsa-miR-4512	CLIP-seq
MIRT1341247	hsa-miR-4668-5p	CLIP-seq
MIRT1341249	hsa-miR-4699-3p	CLIP-seq
MIRT1341250	hsa-miR-4734	CLIP-seq
MIRT2325505	hsa-miR-4753-3p	CLIP-seq
MIRT1341251	hsa-miR-502-5p	CLIP-seq
MIRT1341252	hsa-miR-520d-5p	CLIP-seq
MIRT1341253	hsa-miR-524-5p	CLIP-seq
MIRT1341254	hsa-miR-578	CLIP-seq
MIRT1341255	hsa-miR-581	CLIP-seq
MIRT2325506	hsa-miR-664	CLIP-seq
MIRT1341257	hsa-miR-876-3p	CLIP-seq
MIRT1341236	hsa-miR-1292	CLIP-seq
MIRT1341237	hsa-miR-1296	CLIP-seq
MIRT2325504	hsa-miR-147	CLIP-seq
MIRT2621193	hsa-miR-3611	CLIP-seq
MIRT1341241	hsa-miR-3613-3p	CLIP-seq
MIRT1341242	hsa-miR-3926	CLIP-seq
MIRT1341244	hsa-miR-4471	CLIP-seq
MIRT1341245	hsa-miR-4512	CLIP-seq
MIRT1341246	hsa-miR-4645-5p	CLIP-seq
MIRT1341248	hsa-miR-4673	CLIP-seq
MIRT1341250	hsa-miR-4734	CLIP-seq
MIRT2621194	hsa-miR-4786-3p	CLIP-seq
MIRT1341254	hsa-miR-578	CLIP-seq
MIRT1341255	hsa-miR-581	CLIP-seq
MIRT1341256	hsa-miR-648	CLIP-seq
MIRT1341257	hsa-miR-876-3p	CLIP-seq
MIRT1341236	hsa-miR-1292	CLIP-seq
MIRT1341237	hsa-miR-1296	CLIP-seq
MIRT2325504	hsa-miR-147	CLIP-seq
MIRT2621193	hsa-miR-3611	CLIP-seq
MIRT1341241	hsa-miR-3613-3p	CLIP-seq
MIRT1341242	hsa-miR-3926	CLIP-seq
MIRT1341244	hsa-miR-4471	CLIP-seq
MIRT1341245	hsa-miR-4512	CLIP-seq
MIRT1341246	hsa-miR-4645-5p	CLIP-seq
MIRT1341248	hsa-miR-4673	CLIP-seq
MIRT1341250	hsa-miR-4734	CLIP-seq
MIRT2621194	hsa-miR-4786-3p	CLIP-seq
MIRT1341254	hsa-miR-578	CLIP-seq
MIRT1341255	hsa-miR-581	CLIP-seq
MIRT1341256	hsa-miR-648	CLIP-seq
MIRT1341257	hsa-miR-876-3p	CLIP-seq

Show/Hide all (32)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	9731529, 11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	27720643, 29360106, 32494006, 34822310, 36797247
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	31744343
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0005515	Function	Protein binding	IPI	16189514, 17332742, 22113938, 22365833, 23455924, 24965446, 25737013, 26030138, 27905398, 28514442, 32296183, 32814053, 33961781, 35271311, 39251607
GO:0005634	Component	Nucleus	IDA	27720643, 29360106
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	31744343
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IDA	9731529
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	NAS	31744343
GO:0005681	Component	Spliceosomal complex	TAS	8566756
GO:0005684	Component	U2-type spliceosomal complex	IBA
GO:0005684	Component	U2-type spliceosomal complex	IDA	32494006, 34822310, 36797247
GO:0005684	Component	U2-type spliceosomal complex	IPI	27720643
GO:0005686	Component	U2 snRNP	IBA
GO:0005686	Component	U2 snRNP	NAS	31744343
GO:0005689	Component	U12-type spliceosomal complex	IBA
GO:0005689	Component	U12-type spliceosomal complex	IDA	15146077
GO:0006397	Process	MRNA processing	IEA
GO:0006397	Process	MRNA processing	TAS	8566756
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	8566756
GO:0016607	Component	Nuclear speck	IDA
GO:0016607	Component	Nuclear speck	IEA
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	29360106
GO:0071011	Component	Precatalytic spliceosome	IBA
GO:0071013	Component	Catalytic step 2 spliceosome	IBA
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638
GO:1903241	Process	U2-type prespliceosome assembly	NAS	31744343

MIM	HGNC	e!Ensembl
605591	10769	ENSG00000087365

Q13435

Protein name

Splicing factor 3B subunit 2 (Pre-mRNA-splicing factor SF3b 145 kDa subunit) (SF3b145) (Spliceosome-associated protein 145) (SAP 145)

Protein function

Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:12234937, PubMed:32494006, PubMed:34822310). The 17S U2 SnRNP complex (1) directly participates i

PDB

2DO5 , 5Z56 , 5Z57 , 5Z58 , 6AH0 , 6AHD , 6FF4 , 6FF7 , 6QX9 , 6Y50 , 6Y53 , 6Y5Q , 7ABG , 7ABH , 7ABI , 7DVQ , 7EVO , 7ONB , 7Q3L , 7Q4O , 7Q4P , 7QTT , 7VPX , 8CH6 , 8H6E , 8H6J , 8H6K , 8H6L , 8HK1 , 8I0P , 8I0R , 8I0S , 8I0T , 8I0U , 8I0V , 8QO9 , 8QXD , 8QZS , 8R08 , 8R09 , 8R0A , 8R0B , 8RM5 , 8Y7E

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02037	SAP	24 → 58	SAP domain	Family
PF04037	DUF382	470 → 596	Domain of unknown function (DUF382)	Family
PF04046	PSP	605 → 655	PSP	Family

Sequence

MATEHPEPPKAELQLPPPPPPGHYGAWAAQELQAKLAEIGAPIQGNREELVERLQSYTRQ
TGIVLNRPVLRGEDGDKAAPPPMSAQLPGIPMPPPPLGLPPLQPPPPPPPPPPGLGLGFP
MAHPPNLGPPPPLRVGEPVALSEEERLKLAQQQAALLMQQEERAKQQGDHSLKEHELLEQ
QKRAAVLLEQERQQEIAKMGTPVPRPPQDMGQIGVRTPLGPRVAAPVGPVGPTPTVLPMG
APVPRPRGPPPPPGDENREMDDPSVGPKIPQALEKILQLKESRQEEMNSQQEEEEMETDA
RSSLGQSASETEEDTVSVSKKEKNRKRRNRKKKKKPQRVRGVSSESSGDREKDSTRSRGS
DSPAADVEIEYVTEEPEIYEPNFIFFKRIFEAFKLTDDVKKEKEKEPEKLDKLENSAAPK
KKGFEEEHKDSDDDSSDDEQEKKPEAPKLSKKKLRRMNRFTVAELKQLVARPDVVEMHDV
TAQDPKLLVHLKATRNSVPVPRHWCFKRKYLQGKRGIEKPPFELPDFIKRTGIQEMREAL
QEKEEQKTMKSKMREKVRPKMGKIDIDYQKLHDAFFKWQTKPKLTIHGDLYYEGKEFETR
LKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYGPPPSYPNLKIPGLNSPIPES
CSFGYHAGGWGKPPVDETGKPLYGDVFGTNAAEFQTKTEEEEIDRTPWGELEPSDEESSE
EEEEEESDEDKPDETGFITPADSGLITPGGFSSVPAGMETPELIELRKKKIEEAMDGSET
PQLFTVLPEKRTATVGGAMMGSTHIYDMSTVMSRKGPAPELQGVEVALAPEELELDPMAM
TQKYEEHVREQQAQVEKEDFSDMVAEHAAKQKQKKRKAQPQDSRGGSKKYKEFKF

Sequence length

895

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		mRNA Splicing - Major Pathway mRNA Splicing - Minor Pathway

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Craniofacial microsomia 1	Pathogenic	rs2135050433, rs2135051009, rs2135031513, rs2134479545, rs2496000368	RCV004576998 RCV004576999 RCV004577000 RCV004577001 RCV004595073	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
GOLDENHAR SYNDROME	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEMIFACIAL MICROSOMIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SF3B2-related disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (28)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acral Lentiginous Malignant Melanoma	Acral Lentiginous Malignant Melanoma	BEFREE	22175696		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of pancreas	Pancreatic adenocarcinoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
AURAL ATRESIA, CONGENITAL	Aural Atresia, Congenital	BEFREE	28671284		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular Diseases	BEFREE	30425080, 30425088		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cat eye syndrome	Cat Eye Syndrome	BEFREE	23794175		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of lung	Pulmonary hypoplasia	BEFREE	22750194		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital malformation syndrome	Congenital Malformation Syndrome	BEFREE	29887198		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congestive heart failure	Congestive Heart Failure	BEFREE	28871622		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cutaneous Melanoma	Melanoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphism	Dysmorphism	BEFREE	11810276		★★★★★ ★☆☆☆☆ Found in Text Mining only
Goldenhar Syndrome	Goldenhar syndrome	Pubtator	37555391	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Heart failure	Heart Failure	BEFREE	28871622		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	31348270	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Meningioma	Malignant Meningioma	BEFREE	8434704		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	31431456		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	31431456		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mandibulofacial Dysostosis	Mandibulofacial Dysostosis	BEFREE	28643921		★★★★★ ★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	22175696		★★★★★ ★☆☆☆☆ Found in Text Mining only
MYELODYSPLASTIC SYNDROME	Myelodysplastic Syndrome	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	25645911, 31431456, 8434704		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	31431456		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	31348270	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only

SF3B2 (splicing factor 3b subunit 2)