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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	10262
Gene name Gene Name - the full gene name approved by the HGNC.	Splicing factor 3b subunit 4
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SF3B4
Synonyms (NCBI Gene) Gene synonyms aliases	AFD1, Hsh49, SAP49, SF3b49
Disease Acronyms (UniProt) Disease acronyms from UniProt database	AFD1
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q21.2
Summary Summary of gene provided in NCBI Entrez Gene.	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

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000375	Process	RNA splicing, via transesterification reactions	TAS	7958871
GO:0000398	Process	MRNA splicing, via spliceosome	IC	9731529
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	29360106
GO:0000398	Process	MRNA splicing, via spliceosome	TAS
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0005515	Function	Protein binding	IPI	16189514, 17474147, 21516116, 21988832, 22365833, 25416956, 25737013, 26871637, 29892012, 31515488, 32296183
GO:0005634	Component	Nucleus	IDA	27720643, 28541300, 29360106
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IDA	9731529
GO:0005689	Component	U12-type spliceosomal complex	IBA	21873635
GO:0005689	Component	U12-type spliceosomal complex	IDA	15146077
GO:0005730	Component	Nucleolus	IBA	21873635
GO:0006397	Process	MRNA processing	TAS	7958871
GO:0008380	Process	RNA splicing	TAS	7958871
GO:0048026	Process	Positive regulation of mRNA splicing, via spliceosome	IBA	21873635
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	29360106
GO:1990935	Function	Splicing factor binding	IDA	27720643, 28541300

MIM	HGNC	e!Ensembl
605593	10771	ENSG00000143368

Protein

UniProt ID

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 (14)

Disease term	Disease name	dbSNP ID	References
Causal
Acrofacial dysostosis	Acrofacial dysostosis Rodriguez type, Acrofacial dysostosis, Rodr�guez type	rs794729674, rs875989814, rs1064795108, rs1377622831	27642715
Hearing loss	Conductive hearing loss	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359 View all (184 more)
Hirschsprung disease	Hirschsprung Disease	rs76262710, rs75996173, rs77316810, rs75076352, rs76534745, rs76764689, rs76449634, rs377767412, rs193922699, rs75030001, rs606231342, rs1553540620, rs759944122, rs1057519322, rs1057519323 View all (4 more)
Hydrocephalus	Hydrocephalus	rs387907320, rs369384363, rs387907321, rs372127610, rs770273135, rs797045095, rs797045707, rs769795916, rs781251438, rs922703465, rs376078512, rs1567043467, rs1587149916, rs1586841546
Microcephaly	Microcephaly	rs397704721, rs267607176, rs267607177, rs397704725, rs267606717, rs267606718, rs199422202, rs121434311, rs199422203, rs199422126, rs387906274, rs121434305, rs199422125, rs199422135, rs189678019 View all (280 more)
Multiple congenital anomalies	Multiple congenital anomalies	rs1057517732	24715698, 24003905, 18000904, 23568615, 22541558, 27642715
Nager syndrome	Nager syndrome	rs387907185, rs387907186, rs797045125, rs397515324, rs797045121, rs797045122, rs797045123, rs797045124, rs797045126, rs797045127, rs797045128, rs797045129, rs797045130, rs797045131, rs797045132 View all (6 more)	22541558, 24003905
Osteochondrodysplasia	Osteochondrodysplasias	rs386833498, rs104893919, rs104893916, rs386833492, rs121908078, rs386833497, rs386833507, rs200963884, rs121908077, rs786204675, rs763198695, rs1554095433, rs766836061
Phocomelia	Phocomelia	rs104893835, rs387907231, rs397514643, rs397514666, rs879255548
Polymicrogyria	Polymicrogyria	rs1558010146, rs1558003446, rs1575508937
Radioulnar synostosis	Radioulnar Synostosis	rs1595756416, rs1595756703, rs1231501584, rs1595756962, rs1595757203, rs1595763070, rs1595766210
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085
Skeletal dysplasia	Skeletal dysplasia	rs121912632, rs121912633, rs121912634, rs121912636, rs121912637, rs267607147, rs387906324, rs267607150, rs397514473, rs398123438, rs515726153, rs515726154, rs515726162, rs515726163, rs515726172, rs757011098 View all (1 more)
Tetralogy of fallot	Tetralogy of Fallot	rs28939668, rs727504412, rs864321649, rs774966208, rs876660981, rs886044220, rs1114167357, rs1569484126, rs1569484164, rs1569484122, rs1569484124, rs1569484042, rs1569484120, rs1569484299, rs1569484301, rs1569484288 View all (1 more)

Show/Hide Unknown Diseases (4)

Disease term	Disease name	Source
Unknown
Ptosis	Blepharoptosis, Ptosis	ClinVar
Acrofacial Dysostosis	Nager acrofacial dysostosis, acrofacial dysostosis Rodriguez type	GenCC
Metabolic Syndrome	Metabolic Syndrome	GWAS
Diabetes	Diabetes	GWAS

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text Mining
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)