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	51119
Gene name	SBDS ribosome maturation factor
Gene symbol	SBDS
Synonyms (NCBI Gene)	CGI-97SDO1SDSSWDS
Chromosome	7
Chromosome location	7q11.21
Summary	This gene encodes a highly conserved protein that plays an essential role in ribosome biogenesis. The encoded protein interacts with elongation factor-like GTPase 1 to disassociate eukaryotic initiation factor 6 from the late cytoplasmic pre-60S ribosomal

Show/Hide all (13)

SNP ID	Visualize variation	Clinical significance	Consequence
rs113993991	TA>AG	Pathogenic	Coding sequence variant, stop gained
rs113993992	C>G	Pathogenic	Splice donor variant
rs113993993	A>C,G	Risk-factor, pathogenic	Splice donor variant
rs113993994	CTTT>-	Pathogenic	Coding sequence variant, frameshift variant
rs113993995	C>G	Pathogenic	Missense variant, coding sequence variant
rs113993997	C>G,T	Pathogenic	Splice donor variant
rs113993998	G>A	Pathogenic	Coding sequence variant, stop gained
rs120074160	T>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs201070132	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs774976459	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs779179610	TCT>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs1554341061	->A	Likely-pathogenic	Splice donor variant
rs1584437592	A>G	Likely-pathogenic	Missense variant, coding sequence variant

170

Show/Hide all (170)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016171	hsa-miR-590-3p	Sequencing	20371350
MIRT051786	hsa-let-7c-5p	CLASH	23622248
MIRT1326686	hsa-miR-103a	CLIP-seq
MIRT1326687	hsa-miR-107	CLIP-seq
MIRT1326688	hsa-miR-1183	CLIP-seq
MIRT1326689	hsa-miR-1208	CLIP-seq
MIRT1326690	hsa-miR-1271	CLIP-seq
MIRT1326691	hsa-miR-1297	CLIP-seq
MIRT1326692	hsa-miR-140-3p	CLIP-seq
MIRT1326693	hsa-miR-140-5p	CLIP-seq
MIRT1326694	hsa-miR-182	CLIP-seq
MIRT1326695	hsa-miR-183	CLIP-seq
MIRT1326696	hsa-miR-22	CLIP-seq
MIRT1326697	hsa-miR-26a	CLIP-seq
MIRT1326698	hsa-miR-26b	CLIP-seq
MIRT1326699	hsa-miR-3159	CLIP-seq
MIRT1326700	hsa-miR-335	CLIP-seq
MIRT1326701	hsa-miR-3657	CLIP-seq
MIRT1326702	hsa-miR-3668	CLIP-seq
MIRT1326703	hsa-miR-3684	CLIP-seq
MIRT1326704	hsa-miR-374a	CLIP-seq
MIRT1326705	hsa-miR-374b	CLIP-seq
MIRT1326706	hsa-miR-3910	CLIP-seq
MIRT1326707	hsa-miR-3922-5p	CLIP-seq
MIRT1326708	hsa-miR-3924	CLIP-seq
MIRT1326709	hsa-miR-3978	CLIP-seq
MIRT1326710	hsa-miR-4330	CLIP-seq
MIRT1326711	hsa-miR-4465	CLIP-seq
MIRT1326712	hsa-miR-4496	CLIP-seq
MIRT1326713	hsa-miR-4662a-3p	CLIP-seq
MIRT1326714	hsa-miR-4666-3p	CLIP-seq
MIRT1326715	hsa-miR-4669	CLIP-seq
MIRT1326716	hsa-miR-4803	CLIP-seq
MIRT1326717	hsa-miR-488	CLIP-seq
MIRT1326718	hsa-miR-5096	CLIP-seq
MIRT1326719	hsa-miR-548aa	CLIP-seq
MIRT1326720	hsa-miR-548ag	CLIP-seq
MIRT1326721	hsa-miR-548ai	CLIP-seq
MIRT1326722	hsa-miR-548m	CLIP-seq
MIRT1326723	hsa-miR-550b	CLIP-seq
MIRT1326724	hsa-miR-558	CLIP-seq
MIRT1326725	hsa-miR-568	CLIP-seq
MIRT1326726	hsa-miR-579	CLIP-seq
MIRT1326727	hsa-miR-651	CLIP-seq
MIRT1326728	hsa-miR-873	CLIP-seq
MIRT1326729	hsa-miR-885-3p	CLIP-seq
MIRT1326730	hsa-miR-96	CLIP-seq
MIRT1553227	hsa-miR-323-3p	CLIP-seq
MIRT1553228	hsa-miR-4725-5p	CLIP-seq
MIRT1553229	hsa-miR-504	CLIP-seq
MIRT1326686	hsa-miR-103a	CLIP-seq
MIRT1326687	hsa-miR-107	CLIP-seq
MIRT1326688	hsa-miR-1183	CLIP-seq
MIRT1326695	hsa-miR-183	CLIP-seq
MIRT1326696	hsa-miR-22	CLIP-seq
MIRT1553227	hsa-miR-323-3p	CLIP-seq
MIRT1326700	hsa-miR-335	CLIP-seq
MIRT2097000	hsa-miR-3613-5p	CLIP-seq
MIRT1326710	hsa-miR-4330	CLIP-seq
MIRT1553228	hsa-miR-4725-5p	CLIP-seq
MIRT2097001	hsa-miR-4731-3p	CLIP-seq
MIRT2097002	hsa-miR-4801	CLIP-seq
MIRT1326717	hsa-miR-488	CLIP-seq
MIRT1553229	hsa-miR-504	CLIP-seq
MIRT1326718	hsa-miR-5096	CLIP-seq
MIRT1326720	hsa-miR-548ag	CLIP-seq
MIRT1326721	hsa-miR-548ai	CLIP-seq
MIRT1326722	hsa-miR-548m	CLIP-seq
MIRT1326723	hsa-miR-550b	CLIP-seq
MIRT1326724	hsa-miR-558	CLIP-seq
MIRT1326725	hsa-miR-568	CLIP-seq
MIRT1326726	hsa-miR-579	CLIP-seq
MIRT1326728	hsa-miR-873	CLIP-seq
MIRT1326729	hsa-miR-885-3p	CLIP-seq
MIRT1326690	hsa-miR-1271	CLIP-seq
MIRT1326692	hsa-miR-140-3p	CLIP-seq
MIRT1326694	hsa-miR-182	CLIP-seq
MIRT1326699	hsa-miR-3159	CLIP-seq
MIRT1553227	hsa-miR-323-3p	CLIP-seq
MIRT2097000	hsa-miR-3613-5p	CLIP-seq
MIRT2321365	hsa-miR-3667-5p	CLIP-seq
MIRT1326703	hsa-miR-3684	CLIP-seq
MIRT2321366	hsa-miR-4252	CLIP-seq
MIRT1326710	hsa-miR-4330	CLIP-seq
MIRT1326712	hsa-miR-4496	CLIP-seq
MIRT2321367	hsa-miR-4503	CLIP-seq
MIRT1553228	hsa-miR-4725-5p	CLIP-seq
MIRT1553229	hsa-miR-504	CLIP-seq
MIRT1326725	hsa-miR-568	CLIP-seq
MIRT1326727	hsa-miR-651	CLIP-seq
MIRT1326728	hsa-miR-873	CLIP-seq
MIRT1326730	hsa-miR-96	CLIP-seq
MIRT1326689	hsa-miR-1208	CLIP-seq
MIRT2617601	hsa-miR-1260	CLIP-seq
MIRT2617602	hsa-miR-1260b	CLIP-seq
MIRT2617603	hsa-miR-188-3p	CLIP-seq
MIRT2617604	hsa-miR-191	CLIP-seq
MIRT2617605	hsa-miR-3156-3p	CLIP-seq
MIRT1326699	hsa-miR-3159	CLIP-seq
MIRT2617606	hsa-miR-3198	CLIP-seq
MIRT2097000	hsa-miR-3613-5p	CLIP-seq
MIRT2617607	hsa-miR-3646	CLIP-seq
MIRT1326701	hsa-miR-3657	CLIP-seq
MIRT2321365	hsa-miR-3667-5p	CLIP-seq
MIRT1326702	hsa-miR-3668	CLIP-seq
MIRT2617608	hsa-miR-3671	CLIP-seq
MIRT1326703	hsa-miR-3684	CLIP-seq
MIRT2617609	hsa-miR-371-3p	CLIP-seq
MIRT1326704	hsa-miR-374a	CLIP-seq
MIRT1326705	hsa-miR-374b	CLIP-seq
MIRT2617610	hsa-miR-378	CLIP-seq
MIRT2617611	hsa-miR-378b	CLIP-seq
MIRT2617612	hsa-miR-378c	CLIP-seq
MIRT2617613	hsa-miR-378d	CLIP-seq
MIRT2617614	hsa-miR-378e	CLIP-seq
MIRT2617615	hsa-miR-378f	CLIP-seq
MIRT2617616	hsa-miR-378h	CLIP-seq
MIRT2617617	hsa-miR-378i	CLIP-seq
MIRT1326708	hsa-miR-3924	CLIP-seq
MIRT2617618	hsa-miR-422a	CLIP-seq
MIRT2321366	hsa-miR-4252	CLIP-seq
MIRT2617619	hsa-miR-4261	CLIP-seq
MIRT2617620	hsa-miR-4307	CLIP-seq
MIRT2617621	hsa-miR-4309	CLIP-seq
MIRT2617622	hsa-miR-432	CLIP-seq
MIRT1326712	hsa-miR-4496	CLIP-seq
MIRT2617623	hsa-miR-4638-3p	CLIP-seq
MIRT2617624	hsa-miR-4653-3p	CLIP-seq
MIRT1326713	hsa-miR-4662a-3p	CLIP-seq
MIRT1326715	hsa-miR-4669	CLIP-seq
MIRT1553228	hsa-miR-4725-5p	CLIP-seq
MIRT2097001	hsa-miR-4731-3p	CLIP-seq
MIRT2617625	hsa-miR-4795-3p	CLIP-seq
MIRT2097002	hsa-miR-4801	CLIP-seq
MIRT2617626	hsa-miR-494	CLIP-seq
MIRT1553229	hsa-miR-504	CLIP-seq
MIRT1326719	hsa-miR-548aa	CLIP-seq
MIRT2617627	hsa-miR-562	CLIP-seq
MIRT1326725	hsa-miR-568	CLIP-seq
MIRT1326727	hsa-miR-651	CLIP-seq
MIRT2617628	hsa-miR-885-5p	CLIP-seq
MIRT2617601	hsa-miR-1260	CLIP-seq
MIRT2617602	hsa-miR-1260b	CLIP-seq
MIRT2617603	hsa-miR-188-3p	CLIP-seq
MIRT2617605	hsa-miR-3156-3p	CLIP-seq
MIRT1326699	hsa-miR-3159	CLIP-seq
MIRT2617606	hsa-miR-3198	CLIP-seq
MIRT1326702	hsa-miR-3668	CLIP-seq
MIRT1326703	hsa-miR-3684	CLIP-seq
MIRT1326704	hsa-miR-374a	CLIP-seq
MIRT1326705	hsa-miR-374b	CLIP-seq
MIRT2617610	hsa-miR-378	CLIP-seq
MIRT2617611	hsa-miR-378b	CLIP-seq
MIRT2617612	hsa-miR-378c	CLIP-seq
MIRT2617613	hsa-miR-378d	CLIP-seq
MIRT2617614	hsa-miR-378e	CLIP-seq
MIRT2617615	hsa-miR-378f	CLIP-seq
MIRT2617616	hsa-miR-378h	CLIP-seq
MIRT2617617	hsa-miR-378i	CLIP-seq
MIRT1326708	hsa-miR-3924	CLIP-seq
MIRT2617618	hsa-miR-422a	CLIP-seq
MIRT2321366	hsa-miR-4252	CLIP-seq
MIRT2617621	hsa-miR-4309	CLIP-seq
MIRT2617622	hsa-miR-432	CLIP-seq
MIRT1326712	hsa-miR-4496	CLIP-seq
MIRT2617623	hsa-miR-4638-3p	CLIP-seq
MIRT2617624	hsa-miR-4653-3p	CLIP-seq
MIRT2617625	hsa-miR-4795-3p	CLIP-seq
MIRT1326719	hsa-miR-548aa	CLIP-seq
MIRT1326727	hsa-miR-651	CLIP-seq

Show/Hide all (27)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000922	Component	Spindle pole	IDA	18324336, 19759903
GO:0001833	Process	Inner cell mass cell proliferation	IEA
GO:0002244	Process	Hematopoietic progenitor cell differentiation	IMP	19759903
GO:0003723	Function	RNA binding	HDA	22658674
GO:0005515	Function	Protein binding	IPI	17475909, 17643419, 20015955, 21044950, 26871637, 30545121, 39251607
GO:0005634	Component	Nucleus	IDA	15860664, 18324336
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005730	Component	Nucleolus	IDA	15860664, 17475909
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IDA	15860664, 18324336
GO:0005737	Component	Cytoplasm	IEA
GO:0005819	Component	Spindle	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0006364	Process	RRNA processing	IMP	17643419
GO:0007052	Process	Mitotic spindle organization	IDA	18324336
GO:0008017	Function	Microtubule binding	IDA	18324336
GO:0019843	Function	RRNA binding	IDA	17475909
GO:0030282	Process	Bone mineralization	IMP	17920346
GO:0030595	Process	Leukocyte chemotaxis	IDA	14743349
GO:0042254	Process	Ribosome biogenesis	IEA
GO:0042256	Process	Cytosolic ribosome assembly	IDA	21536732
GO:0042256	Process	Cytosolic ribosome assembly	IEA
GO:0043022	Function	Ribosome binding	IDA	21536732
GO:0048539	Process	Bone marrow development	IMP	15342903

MIM	HGNC	e!Ensembl
607444	19440	ENSG00000126524

Q9Y3A5

Protein name

Ribosome maturation protein SBDS (Shwachman-Bodian-Diamond syndrome protein)

Protein function

Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFL1, triggers the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80

PDB

2KDO , 2L9N , 5AN9 , 5ANB , 5ANC , 6QKL

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01172	SBDS	14 → 101	Shwachman-Bodian-Diamond syndrome (SBDS) protein	Family
PF09377	SBDS_C	107 → 225	SBDS protein C-terminal domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed.

Sequence

MSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNV
SKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCV
NPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIERAHMRLRFILPV
NEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDELIKKETKGKGSLEVLNLK
DVEEGDEKFE

Sequence length

250

Interactions

View interactions

	KEGG
	Ribosome biogenesis in eukaryotes

162

Show/Hide Causal Diseases (24)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Acute myeloid leukemia	Likely pathogenic; Pathogenic	rs113993993	RCV005887242
Agenesis of permanent teeth	Likely pathogenic; Pathogenic	rs113993993, rs120074160	RCV000626935 RCV000626934
Aplastic anemia	Likely pathogenic; Pathogenic	rs1411636529, rs113993991, rs113993993, rs373730800, rs113993990, rs2536932418, rs752809798, rs1376011266, rs2536930205, rs2536932390, rs745661722, rs775057252, rs113993997, rs1793080553, rs2536932319 View all (10 more)	RCV003475533 RCV002496241 RCV000763594 RCV003474976 RCV002503966 RCV003472588 RCV003472589 RCV003472590 RCV003472592 RCV003472593 RCV003472594 RCV003472595 RCV003472596 RCV003472597 RCV003472598 RCV003472599 RCV004573555 RCV004573557 RCV000768305 RCV003473117 RCV003315402 RCV003476190 RCV005034065 RCV003476214 RCV003473537
Aplastic anemia, susceptibility to	Likely pathogenic; Pathogenic	rs113993993	RCV000003348
Cervical cancer	Likely pathogenic; Pathogenic	rs113993993	RCV005887247
Colon adenocarcinoma	Likely pathogenic; Pathogenic	rs113993993	RCV005887241
Deeply set eye	Likely pathogenic; Pathogenic	rs113993993, rs120074160	RCV000626935 RCV000626934
Familial pancreatic carcinoma	Likely pathogenic; Pathogenic	rs113993993	RCV005887249
Hepatocellular carcinoma	Likely pathogenic; Pathogenic	rs113993993	RCV005887244
Intellectual disability	Likely pathogenic; Pathogenic	rs113993993, rs120074160	RCV005624667 RCV001293358
Lymphoma	Likely pathogenic; Pathogenic	rs113993993	RCV005887250
Malignant tumor of esophagus	Likely pathogenic; Pathogenic	rs113993993	RCV005887245
Malignant tumor of urinary bladder	Likely pathogenic; Pathogenic	rs113993993	RCV005887243
Microcephaly	Likely pathogenic; Pathogenic	rs113993993, rs120074160	RCV000626935 RCV000626934
Nonpapillary renal cell carcinoma	Likely pathogenic; Pathogenic	rs113993993	RCV005887246
Ovarian cancer	Likely pathogenic; Pathogenic	rs113993993	RCV005887248
Ovarian serous cystadenocarcinoma	Likely pathogenic; Pathogenic	rs113993993	RCV005887251
SBDS-related disorder	Pathogenic; Likely pathogenic	rs113993991, rs113993993, rs113993994	RCV003904800 RCV003407264 RCV003904855
Short stature	Likely pathogenic; Pathogenic	rs113993993, rs120074160	RCV000626935 RCV000626934
Shwachman syndrome	Pathogenic; Likely pathogenic	rs113993991, rs113993993	RCV004017224 RCV001270036
Shwachman-Diamond syndrome 1	Pathogenic; Likely pathogenic	rs1792914342, rs1411636529, rs2129231218, rs113993991, rs113993993, rs2536932431, rs373730800, rs1387962158, rs2536928013, rs113993990, rs2536932418, rs1376011266, rs745661722, rs113993997, rs371133001 View all (8 more)	RCV001335791 RCV003131368 RCV001824235 RCV000003346 RCV000003347 RCV000003350 RCV000206645 RCV003142536 RCV003221317 RCV000020725 RCV005628164 RCV005254798 RCV005036818 RCV005254800 RCV004595036 RCV000020728 RCV000020729 RCV000020732 RCV000020735 RCV000987895 RCV003230528 RCV000995633 RCV000995634 RCV001194601
Splenomegaly	Likely pathogenic; Pathogenic	rs113993993, rs120074160	RCV000626935 RCV000626934
Thyroid cancer, nonmedullary, 1	Likely pathogenic; Pathogenic	rs113993993	RCV005887252
Uterine corpus endometrial carcinoma	Likely pathogenic; Pathogenic	rs113993993	RCV005887253

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Hereditary cancer-predisposing syndrome	Benign	rs113993989	RCV005638404
Melanoma	Conflicting classifications of pathogenicity	rs760364037	RCV005930798

Show/Hide Text Mining Associations (23)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Anemia Aplastic	Associate	17478638
Anemia Diamond Blackfan	Associate	17475909, 21963601
Aneuploidy	Associate	18324336
Bone Marrow Diseases	Associate	22371183
Bone Marrow Failure Disorders	Associate	19016724, 20658628, 34758064, 37450374
Breast Neoplasms	Associate	30792990
Congenital Bone Marrow Failure Syndromes	Associate	18324336
Immunologic Deficiency Syndromes	Associate	17478638
Leukemia	Associate	18324336
Leukemia Myeloid Acute	Associate	19759903
Lung Neoplasms	Associate	37885353
Melanoma	Associate	30792990
Mosaic variegated aneuploidy syndrome	Associate	18324336
Myelodysplastic Syndromes	Associate	22371183, 27418648
Neoplasms	Associate	19016724, 30792990, 37226705, 37885353
Neural Tube Defects	Associate	22371183
Neutropenia	Associate	19759903
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	19222471
Pyle disease	Associate	22554078
Renal Insufficiency	Associate	21963601
Shwachman Diamond Syndrome	Associate	15284109, 15769891, 15870673, 17376717, 17475909, 17478638, 18324336, 19016724, 19222471, 19438500, 19759903, 20053358, 20658628, 21695142, 21803848 View all (12 more)
Shwachman Diamond Syndrome	Inhibit	34948128
Vitamin A Deficiency	Associate	22554078

SBDS (SBDS ribosome maturation factor)