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	10262
Gene name	Splicing factor 3b subunit 4
Gene symbol	SF3B4
Synonyms (NCBI Gene)	AFD1Hsh49SAP49SF3b49
Chromosome	1
Chromosome location	1q21.2
Summary	This gene encodes one of four subunits of the splicing factor 3B. The protein encoded by this gene cross-links to a region in the pre-mRNA immediately upstream of the branchpoint sequence in pre-mRNA in the prespliceosomal complex A. It also may be involv

Show/Hide all (25)

SNP ID	Visualize variation	Clinical significance	Consequence
rs387907185	T>C	Pathogenic	Initiator codon variant, missense variant
rs387907186	G>-,GG	Pathogenic	Coding sequence variant, frameshift variant
rs397515324	G>A	Pathogenic	Coding sequence variant, stop gained
rs782357237	->G	Pathogenic	Coding sequence variant, frameshift variant
rs797044869	C>T	Likely-pathogenic	Splice acceptor variant
rs797045121	CTCGAAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045122	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045123	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045124	->T	Pathogenic	Coding sequence variant, frameshift variant
rs797045125	C>T	Pathogenic	Splice donor variant
rs797045126	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045127	->ATACCCC	Pathogenic	Coding sequence variant, frameshift variant
rs797045128	GGG>-,GG,GGGG	Pathogenic	Coding sequence variant, frameshift variant, inframe deletion
rs797045129	->T	Pathogenic	Coding sequence variant, frameshift variant
rs797045130	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045131	->TGGG	Pathogenic	Coding sequence variant, frameshift variant
rs797045132	G>A	Pathogenic	Coding sequence variant, stop gained
rs797045133	G>T	Pathogenic	Coding sequence variant, stop gained
rs797045134	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045954	TCGAGGGGGAACTGGTGGCC>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045955	C>A	Pathogenic	Coding sequence variant, stop gained
rs797045956	CA>-	Pathogenic	Coding sequence variant, frameshift variant
rs797045957	CACTGGGGGTGGG>-	Pathogenic	Coding sequence variant, frameshift variant
rs886041532	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1553765608	->CAGTGTA	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (34)

miRTarBase ID	miRNA	Experiments	Reference
MIRT051835	hsa-let-7c-5p	CLASH	23622248
MIRT047686	hsa-miR-10a-5p	CLASH	23622248
MIRT042581	hsa-miR-423-3p	CLASH	23622248
MIRT038362	hsa-miR-296-3p	CLASH	23622248
MIRT1341553	hsa-miR-122	CLIP-seq
MIRT1341554	hsa-miR-1914	CLIP-seq
MIRT1341555	hsa-miR-3121-5p	CLIP-seq
MIRT1341556	hsa-miR-3148	CLIP-seq
MIRT1341557	hsa-miR-3190	CLIP-seq
MIRT1341558	hsa-miR-323-3p	CLIP-seq
MIRT1341559	hsa-miR-342-5p	CLIP-seq
MIRT1341560	hsa-miR-3664-3p	CLIP-seq
MIRT1341561	hsa-miR-4436a	CLIP-seq
MIRT1341562	hsa-miR-4447	CLIP-seq
MIRT1341563	hsa-miR-4472	CLIP-seq
MIRT1341564	hsa-miR-4481	CLIP-seq
MIRT1341565	hsa-miR-450b-5p	CLIP-seq
MIRT1341566	hsa-miR-4664-5p	CLIP-seq
MIRT1341567	hsa-miR-4745-5p	CLIP-seq
MIRT1341568	hsa-miR-4766-5p	CLIP-seq
MIRT1341569	hsa-miR-4768-5p	CLIP-seq
MIRT1341570	hsa-miR-4803	CLIP-seq
MIRT1341571	hsa-miR-488	CLIP-seq
MIRT1341572	hsa-miR-510	CLIP-seq
MIRT1341573	hsa-miR-512-5p	CLIP-seq
MIRT1341574	hsa-miR-518a-5p	CLIP-seq
MIRT1341575	hsa-miR-527	CLIP-seq
MIRT1341576	hsa-miR-875-5p	CLIP-seq
MIRT1341565	hsa-miR-450b-5p	CLIP-seq
MIRT1341568	hsa-miR-4766-5p	CLIP-seq
MIRT1341569	hsa-miR-4768-5p	CLIP-seq
MIRT1341571	hsa-miR-488	CLIP-seq
MIRT1341574	hsa-miR-518a-5p	CLIP-seq
MIRT1341575	hsa-miR-527	CLIP-seq

Show/Hide all (33)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000375	Process	RNA splicing, via transesterification reactions	TAS	7958871
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	9731529
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	27720643, 29360106, 32494006, 36797247
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	31744343
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	15105431, 16189514, 17332742, 17474147, 21516116, 21988832, 22365833, 25416956, 25737013, 26871637, 27905398, 29892012, 31515488, 32296183, 35271311, 36217029, 39251607
GO:0005634	Component	Nucleus	IDA	27720643, 28541300, 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	7958871
GO:0005684	Component	U2-type spliceosomal complex	IDA	32494006, 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	IDA	15146077
GO:0006397	Process	MRNA processing	IEA
GO:0006397	Process	MRNA processing	TAS	7958871
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	7958871
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	29360106
GO:0071011	Component	Precatalytic spliceosome	IBA
GO:1903241	Process	U2-type prespliceosome assembly	NAS	31744343
GO:1990935	Function	Splicing factor binding	IDA	27720643, 28541300

MIM	HGNC	e!Ensembl
605593	10771	ENSG00000143368

Q15427

Protein name

Splicing factor 3B subunit 4 (Pre-mRNA-splicing factor SF3b 49 kDa subunit) (Spliceosome-associated protein 49) (SAP 49)

Protein function

Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:10882114, PubMed:12234937, PubMed:27720643, PubMed:32494006). The 17S U2 SnRNP complex (1) direct

PDB

1X5T , 5GVQ , 5Z56 , 5Z57 , 5Z58 , 6AH0 , 6AHD , 6QX9 , 6Y53 , 6Y5Q , 7ABG , 7ABH , 7ABI , 7DVQ , 7EVO , 7ONB , 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
PF00076	RRM_1	15 → 85	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	Domain
PF00076	RRM_1	102 → 173	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	Domain

Sequence

MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE
FLSEEDADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF
SAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK
DSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPP
GSFPPPVPPPGALPPGIPPAMPPPPMPPGAAGHGPPSAGTPGAGHPGHGHSHPHPFPPGG
MPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPPRGPPFGS
PMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLRG
PLPQ

Sequence length

424

Interactions

View interactions

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

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hereditary hearing loss and deafness	Pathogenic	rs797045128	RCV000515537
Nager syndrome	Pathogenic	rs2101646017, rs2101648820, rs2101647799, rs797045121, rs797045122, rs797045123, rs797045124, rs797045126, rs797045127, rs797045128, rs797045129, rs797045130, rs797045131, rs797045132, rs797045133 View all (10 more)	RCV001644990 RCV001376052 RCV001784964 RCV000190847 RCV000190848 RCV000190849 RCV000190850 RCV000190853 RCV000190854 RCV000190855 RCV000190856 RCV000190857 RCV000190858 RCV000190859 RCV000190860 RCV000190861 RCV000192855 RCV000193286 RCV000193888 RCV000195244 RCV003128294 RCV000024344 RCV000024346 RCV000024347 RCV000055627
SF3B4-related disorder	Likely pathogenic	rs2525112539	RCV003982778

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Malignant tumor of urinary bladder	Likely benign	rs782034977	RCV005933399
Sarcoma	Likely benign	rs782034977	RCV005933400

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acrofacial dysostosis Nager type	Associate	22541558, 27622494, 27966544, 32537850, 36639679
Acrofacial dysostosis Rodriguez type	Associate	27622494
Adenocarcinoma of Lung	Associate	35852380, 38168564
Anophthalmos with limb anomalies	Associate	32537850
Breast Neoplasms	Associate	37551622
Carcinogenesis	Associate	28351319, 29397868, 35996826, 36639679, 38168564, 40234915
Carcinoma Hepatocellular	Associate	29397868, 30391496, 31811111, 33411682, 35030977, 40234915
Carcinoma Hepatocellular	Stimulate	37899451
Carcinoma Non Small Cell Lung	Associate	35852380, 35996826
Carcinoma Renal Cell	Associate	36639679
Delayed Cranial Ossification due to CBFB Haploinsufficiency	Associate	22541558
Developmental Disabilities	Associate	27622494
Dysostoses	Associate	27622494
Fibrosis	Associate	31811111
Hearing Loss	Associate	29293505
Lung Neoplasms	Associate	35852380, 35996826
Mandibulofacial Dysostosis	Associate	32537850
Musculoskeletal Abnormalities	Associate	27622494
Myeloproliferative Disorder Chronic with Eosinophilia	Associate	35996826
Neoplasm Metastasis	Associate	30391496
Neoplasms	Inhibit	28351319
Neoplasms	Associate	29397868, 35210412
Neoplasms	Stimulate	35996826
Ovarian Neoplasms	Stimulate	35210412
Pancreatic Neoplasms	Inhibit	28351319
Precancerous Conditions	Associate	29397868

SF3B4 (splicing factor 3b subunit 4)