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

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 (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hereditary hearing loss and deafness	Pathogenic	rs797045128	RCV000515537	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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 View all (20 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SF3B4-related disorder	Likely pathogenic	rs2525112539	RCV003982778	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (8)

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.
ACROFACIAL DYSOSTOSIS RODRIGUEZ TYPE	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HEARING DISORDER	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METAPHYSEAL CHONDRODYSPLASIA SCHMID TYPE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	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 (73)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acrofacial Dysostosis	Acrofacial Dysostosis	BEFREE	24715698, 27622494		★★★★★ ★☆☆☆☆ Found in Text Mining only
Acrofacial dysostosis Rodriguez type	Acrofacial dysostosis	Pubtator	27622494	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Acrofacial dysostosis Rodriguez type	Acrofacial Dysostosis	ORPHANET_DG	27642715		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
	Acrofacial Dysostosis	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Anophthalmos with limb anomalies	Anophthalmia	Pubtator	32537850	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Aqueductal Stenosis	Aqueductal Stenosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Arhinencephaly	Arrhinencephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	37551622	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	28351319, 29397868, 35996826, 36639679, 38168564, 40234915	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	29397868, 30391496, 31811111, 33411682, 35030977, 40234915	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	37899451	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	36639679	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly	Clinodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of radius	Congenital Hypoplasia Of Radius	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	GENOMICS_ENGLAND_DG	24003905		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	27622494	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	18000904, 22541558, 23568615, 24003905, 24715698, 27642715		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysostoses	Dysostoses	BEFREE	27622494		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysostoses	Dysphoric mood	Pubtator	27622494	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastroschisis	Gastroschisis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	29293505	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoplasia of first ribs	Hypoplasia Of Rib	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoplasia of the epiglottis	Hypoplasia of the epiglottis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoplasia of the maxilla	Hypoplasia of the maxilla	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Laryngeal hypoplasia	Laryngeal hypoplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	25731616, 27127115, 29397868, 30391496		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	35852380, 35996826	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrostomia	Macrostomia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	29397868		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	28351319		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mandibulofacial Dysostosis	Mandibulofacial dysostosis	Pubtator	32537850	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple congenital anomalies	Multiple Congenital Anomalies	CLINVAR_DG	18000904, 22541558, 23568615, 24003905, 24715698, 27642715		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myeloproliferative Disorder Chronic with Eosinophilia	Myeloproliferative disorder	Pubtator	35996826	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nager syndrome	Nager Syndrome	BEFREE	22541558, 23568615, 23913624, 24003905, 24715698, 25865758, 26679067, 26874011, 27622494, 27966544, 30924273, 30970347		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nager syndrome	Nager Syndrome	ORPHANET_DG	22541558		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nager syndrome	Nager Syndrome	CLINVAR_DG	22541558		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nager syndrome	Nager Syndrome	GENOMICS_ENGLAND_DG	22541558, 24003905		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nager syndrome	Nager Syndrome	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nager syndrome	Nager Syndrome	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neoplasms	Neoplasms	BEFREE	29397868		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteochondrodysplasias	Osteochondrodysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	35210412	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	28351319		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	28351319	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Phocomelia	Phocomelia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Radioulnar Synostosis	Radioulnar Synostosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Skeletal dysplasia	Skeletal Dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Sprengel deformity	Sprengel Deformity	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Stenosis of external auditory canal	Stenosis Of External Auditory Canal	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Syndactyly of fingers	Syndactyly of fingers	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Syndactyly of the toes	Syndactyly Of The Toes	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Tetralogy of Fallot	Tetralogy of Fallot	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Thumb aplasia	Thumb Aplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Trismus	Trismus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Unilateral agenesis of kidney	Renal aplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Urticaria	Urticaria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Anomalies	Uterine Anomalies	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Velopharyngeal Insufficiency	Velopharyngeal Insufficiency	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

SF3B4 (splicing factor 3b subunit 4)