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.	26276
Gene name Gene Name - the full gene name approved by the HGNC.	VPS33B late endosome and lysosome associated
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	VPS33B
Synonyms (NCBI Gene) Gene synonyms aliases	KDIDAR, PFIC12
Chromosome Chromosome number	15
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	15q26.1
Summary Summary of gene provided in NCBI Entrez Gene.	Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuol

Show/Hide all(28)

SNP ID	Visualize variation	Clinical significance	Consequence
rs11542638	G>A,T	Pathogenic, likely-benign, benign	5 prime UTR variant, coding sequence variant, stop gained, synonymous variant, intron variant, non coding transcript variant, genic upstream transcript variant
rs121434383	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs121434384	G>A,T	Pathogenic	Non coding transcript variant, coding sequence variant, synonymous variant, stop gained
rs139655526	A>G	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs139709507	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs142964161	G>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs145092724	A>C	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs145303578	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs201431055	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant
rs201436915	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, synonymous variant
rs372769808	C>T	Pathogenic	Intron variant, genic upstream transcript variant
rs375376103	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs398122407	C>G	Likely-pathogenic, pathogenic-likely-pathogenic, pathogenic	Intron variant
rs398122408	GT>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs751858602	C>A,T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant, missense variant
rs774529051	T>C	Pathogenic	Splice acceptor variant
rs774653538	C>A,T	Pathogenic	Splice donor variant
rs780626848	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs794726658	C>T	Pathogenic	Splice donor variant
rs886043445	T>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs997425993	C>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs1064793614	A>-	Pathogenic	Frameshift variant, genic upstream transcript variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs1416595652	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, 5 prime UTR variant, genic upstream transcript variant, coding sequence variant, intron variant
rs1442840881	->G	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1555458189	C>T	Pathogenic	Splice donor variant
rs1555459218	C>G	Likely-pathogenic	Synonymous variant, coding sequence variant, non coding transcript variant
rs1596348299	A>G	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1596358564	AG>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant

Show/Hide all(139)

miRTarBase ID	miRNA	Experiments	Reference
MIRT726128	hsa-miR-15a-5p	HITS-CLIP	22473208
MIRT726127	hsa-miR-15b-5p	HITS-CLIP	22473208
MIRT726126	hsa-miR-16-5p	HITS-CLIP	22473208
MIRT726125	hsa-miR-195-5p	HITS-CLIP	22473208
MIRT1486520	hsa-miR-103a	CLIP-seq
MIRT1486521	hsa-miR-107	CLIP-seq
MIRT1486522	hsa-miR-1236	CLIP-seq
MIRT1486523	hsa-miR-15a	CLIP-seq
MIRT1486524	hsa-miR-15b	CLIP-seq
MIRT1486525	hsa-miR-16	CLIP-seq
MIRT1486526	hsa-miR-195	CLIP-seq
MIRT1486527	hsa-miR-3074-5p	CLIP-seq
MIRT1486528	hsa-miR-3613-5p	CLIP-seq
MIRT1486529	hsa-miR-370	CLIP-seq
MIRT1486530	hsa-miR-3940-5p	CLIP-seq
MIRT1486531	hsa-miR-424	CLIP-seq
MIRT1486532	hsa-miR-4507	CLIP-seq
MIRT1486533	hsa-miR-4524	CLIP-seq
MIRT1486534	hsa-miR-497	CLIP-seq
MIRT1486535	hsa-miR-503	CLIP-seq
MIRT1486536	hsa-miR-646	CLIP-seq
MIRT1486523	hsa-miR-15a	CLIP-seq
MIRT1486524	hsa-miR-15b	CLIP-seq
MIRT1486525	hsa-miR-16	CLIP-seq
MIRT1486526	hsa-miR-195	CLIP-seq
MIRT2146307	hsa-miR-2117	CLIP-seq
MIRT2146308	hsa-miR-2278	CLIP-seq
MIRT2146309	hsa-miR-2467-3p	CLIP-seq
MIRT2146310	hsa-miR-3188	CLIP-seq
MIRT2146311	hsa-miR-3200-5p	CLIP-seq
MIRT2146312	hsa-miR-409-3p	CLIP-seq
MIRT1486531	hsa-miR-424	CLIP-seq
MIRT2146313	hsa-miR-4251	CLIP-seq
MIRT2146314	hsa-miR-4273	CLIP-seq
MIRT2146315	hsa-miR-4329	CLIP-seq
MIRT2146316	hsa-miR-4468	CLIP-seq
MIRT1486533	hsa-miR-4524	CLIP-seq
MIRT2146317	hsa-miR-4684-5p	CLIP-seq
MIRT2146318	hsa-miR-4699-3p	CLIP-seq
MIRT1486534	hsa-miR-497	CLIP-seq
MIRT1486536	hsa-miR-646	CLIP-seq
MIRT1486520	hsa-miR-103a	CLIP-seq
MIRT1486521	hsa-miR-107	CLIP-seq
MIRT1486523	hsa-miR-15a	CLIP-seq
MIRT1486524	hsa-miR-15b	CLIP-seq
MIRT1486525	hsa-miR-16	CLIP-seq
MIRT2366782	hsa-miR-181a	CLIP-seq
MIRT2366783	hsa-miR-181b	CLIP-seq
MIRT2366784	hsa-miR-181c	CLIP-seq
MIRT2366785	hsa-miR-181d	CLIP-seq
MIRT1486526	hsa-miR-195	CLIP-seq
MIRT1486528	hsa-miR-3613-5p	CLIP-seq
MIRT1486530	hsa-miR-3940-5p	CLIP-seq
MIRT1486531	hsa-miR-424	CLIP-seq
MIRT2366786	hsa-miR-4262	CLIP-seq
MIRT1486532	hsa-miR-4507	CLIP-seq
MIRT1486533	hsa-miR-4524	CLIP-seq
MIRT2146318	hsa-miR-4699-3p	CLIP-seq
MIRT1486534	hsa-miR-497	CLIP-seq
MIRT1486535	hsa-miR-503	CLIP-seq
MIRT1486536	hsa-miR-646	CLIP-seq
MIRT1486533	hsa-miR-4524	CLIP-seq
MIRT2660423	hsa-miR-1	CLIP-seq
MIRT1486520	hsa-miR-103a	CLIP-seq
MIRT1486521	hsa-miR-107	CLIP-seq
MIRT1486522	hsa-miR-1236	CLIP-seq
MIRT2660424	hsa-miR-141	CLIP-seq
MIRT1486523	hsa-miR-15a	CLIP-seq
MIRT1486524	hsa-miR-15b	CLIP-seq
MIRT1486525	hsa-miR-16	CLIP-seq
MIRT2366782	hsa-miR-181a	CLIP-seq
MIRT2366783	hsa-miR-181b	CLIP-seq
MIRT2366784	hsa-miR-181c	CLIP-seq
MIRT2366785	hsa-miR-181d	CLIP-seq
MIRT2660425	hsa-miR-193a-3p	CLIP-seq
MIRT2660426	hsa-miR-193b	CLIP-seq
MIRT1486526	hsa-miR-195	CLIP-seq
MIRT2660427	hsa-miR-200a	CLIP-seq
MIRT2660428	hsa-miR-206	CLIP-seq
MIRT1486527	hsa-miR-3074-5p	CLIP-seq
MIRT2660429	hsa-miR-3127-5p	CLIP-seq
MIRT1486529	hsa-miR-370	CLIP-seq
MIRT1486531	hsa-miR-424	CLIP-seq
MIRT2366786	hsa-miR-4262	CLIP-seq
MIRT2660430	hsa-miR-4270	CLIP-seq
MIRT2660431	hsa-miR-4441	CLIP-seq
MIRT1486533	hsa-miR-4524	CLIP-seq
MIRT2660432	hsa-miR-4668-5p	CLIP-seq
MIRT2660433	hsa-miR-4743	CLIP-seq
MIRT2660434	hsa-miR-4766-3p	CLIP-seq
MIRT1486534	hsa-miR-497	CLIP-seq
MIRT1486535	hsa-miR-503	CLIP-seq
MIRT2660435	hsa-miR-505	CLIP-seq
MIRT2660436	hsa-miR-548p	CLIP-seq
MIRT2660437	hsa-miR-613	CLIP-seq
MIRT1486536	hsa-miR-646	CLIP-seq
MIRT2660423	hsa-miR-1	CLIP-seq
MIRT1486520	hsa-miR-103a	CLIP-seq
MIRT1486521	hsa-miR-107	CLIP-seq
MIRT1486522	hsa-miR-1236	CLIP-seq
MIRT2695064	hsa-miR-1343	CLIP-seq
MIRT2660424	hsa-miR-141	CLIP-seq
MIRT1486523	hsa-miR-15a	CLIP-seq
MIRT1486524	hsa-miR-15b	CLIP-seq
MIRT1486525	hsa-miR-16	CLIP-seq
MIRT2366782	hsa-miR-181a	CLIP-seq
MIRT2366783	hsa-miR-181b	CLIP-seq
MIRT2366784	hsa-miR-181c	CLIP-seq
MIRT2366785	hsa-miR-181d	CLIP-seq
MIRT2660425	hsa-miR-193a-3p	CLIP-seq
MIRT2660426	hsa-miR-193b	CLIP-seq
MIRT1486526	hsa-miR-195	CLIP-seq
MIRT2660427	hsa-miR-200a	CLIP-seq
MIRT2660428	hsa-miR-206	CLIP-seq
MIRT1486527	hsa-miR-3074-5p	CLIP-seq
MIRT2660429	hsa-miR-3127-5p	CLIP-seq
MIRT2695065	hsa-miR-3192	CLIP-seq
MIRT1486528	hsa-miR-3613-5p	CLIP-seq
MIRT1486529	hsa-miR-370	CLIP-seq
MIRT1486530	hsa-miR-3940-5p	CLIP-seq
MIRT1486531	hsa-miR-424	CLIP-seq
MIRT2366786	hsa-miR-4262	CLIP-seq
MIRT2660430	hsa-miR-4270	CLIP-seq
MIRT2695066	hsa-miR-4300	CLIP-seq
MIRT2695067	hsa-miR-4311	CLIP-seq
MIRT2660431	hsa-miR-4441	CLIP-seq
MIRT1486532	hsa-miR-4507	CLIP-seq
MIRT1486533	hsa-miR-4524	CLIP-seq
MIRT2660432	hsa-miR-4668-5p	CLIP-seq
MIRT2660433	hsa-miR-4743	CLIP-seq
MIRT2660434	hsa-miR-4766-3p	CLIP-seq
MIRT1486534	hsa-miR-497	CLIP-seq
MIRT1486535	hsa-miR-503	CLIP-seq
MIRT2660435	hsa-miR-505	CLIP-seq
MIRT2695068	hsa-miR-539	CLIP-seq
MIRT2660436	hsa-miR-548p	CLIP-seq
MIRT2660437	hsa-miR-613	CLIP-seq
MIRT1486536	hsa-miR-646	CLIP-seq
MIRT2695069	hsa-miR-920	CLIP-seq

Show/Hide all(50)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	16189514, 18474358, 19109425, 20190753, 22677173, 23901104, 23918659, 25416956, 25783203, 26871637, 28017832, 29778605, 32296183
GO:0005737	Component	Cytoplasm	IDA	15052268, 20190753
GO:0005764	Component	Lysosome	IBA
GO:0005764	Component	Lysosome	IDA	15052268
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IDA	23918659
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IEA
GO:0005770	Component	Late endosome	IDA	15052268
GO:0005794	Component	Golgi apparatus	IDA	27435297
GO:0005829	Component	Cytosol	TAS
GO:0006886	Process	Intracellular protein transport	IBA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0007032	Process	Endosome organization	IMP	23918659
GO:0008333	Process	Endosome to lysosome transport	IMP	25783203
GO:0010008	Component	Endosome membrane	TAS
GO:0015031	Process	Protein transport	IEA
GO:0015031	Process	Protein transport	IMP	15052268
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IBA
GO:0016192	Process	Vesicle-mediated transport	IDA	15790593
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0017185	Process	Peptidyl-lysine hydroxylation	IMP	27435297
GO:0030136	Component	Clathrin-coated vesicle	IDA	21411634
GO:0030136	Component	Clathrin-coated vesicle	IEA
GO:0030199	Process	Collagen fibril organization	IEA
GO:0030897	Component	HOPS complex	IDA	25783203
GO:0030897	Component	HOPS complex	IDA	19109425
GO:0031091	Component	Platelet alpha granule	IDA	16123220
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031901	Component	Early endosome membrane	IDA	21411634
GO:0031902	Component	Late endosome membrane	IEA
GO:0032400	Process	Melanosome localization	IDA	15790593
GO:0032418	Process	Lysosome localization	IDA	15790593
GO:0032963	Process	Collagen metabolic process	IEA
GO:0032963	Process	Collagen metabolic process	IMP	27435297
GO:0033263	Component	CORVET complex	IBA
GO:0035855	Process	Megakaryocyte development	IEA
GO:0043589	Process	Skin morphogenesis	IMP	28017832
GO:0044877	Function	Protein-containing complex binding	IPI	21411634
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	19109425
GO:0055037	Component	Recycling endosome	IEA
GO:0061025	Process	Membrane fusion	IMP	15052268
GO:0070889	Process	Platelet alpha granule organization	IEA
GO:0070889	Process	Platelet alpha granule organization	IMP	16123220
GO:0090330	Process	Regulation of platelet aggregation	IEA
GO:0090385	Process	Phagosome-lysosome fusion	NAS	27555442
GO:0097352	Process	Autophagosome maturation	IMP	25783203
GO:0099023	Component	Vesicle tethering complex	IPI	23918659

MIM	HGNC	e!Ensembl
608552	12712	ENSG00000184056

Protein

UniProt ID

Q9H267

Protein name

Vacuolar protein sorting-associated protein 33B (hVPS33B)

Protein function

May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane docking/fusion reactions of late endosomes/lysosomes. Required for proper trafficking and targeting of the collagen-modifying enzyme lysyl hydroxyl

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00995	Sec1	37 → 611	Sec1 family	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous; highly expressed in testis and low expression in the lung.

Sequence

MAFPHRPDAPELPDFSMLKRLARDQLIYLLEQLPGKKDLFIEADLMSPLDRIANVSILKQ
HEVDKLYKVENKPALSSNEQLCFLVRPRIKNMRYIASLVNADKLAGRTRKYKVIFSPQKF
YACEMVLEEEGIYGDVSCDEWAFSLLPLDVDLLSMELPEFFRDYFLEGDQRWINTVAQAL
HLLSTLYGPFPNCYGIGRCAKMAYELWRNLEEEEDGETKGRRPEIGHIFLLDRDVDFVTA
LCSQVVYEGLVDDTFRIKCGSVDFGPEVTSSDKSLKVLLNAEDKVFNEIRNEHFSNVFGF
LSQKARNLQAQYDRRRGMDIKQMKNFVSQELKGLKQEHRLLSLHIGACESIMKKKTKQDF
QELIKTEHALLEGFNIRESTSYIEEHIDRQVSPIESLRLMCLLSITENGLIPKDYRSLKT
QYLQSYGPEHLLTFSNLRRAGLLTEQAPGDTLTAVESKVSKLVTDKAAGKITDAFSSLAK
RSNFRAISKKLNLIPRVDGEYDLKVPRDMAYVFGGAYVPLSCRIIEQVLERRSWQGLDEV
VRLLNCSDFAFTDMTKEDKASSESLRLILVVFLGGCTFSEISALRFLGREKGYRFIFLTT
AVTNSARLMEAMSEVKA

Sequence length

617

Interactions

View interactions

	Reactome
			Prevention of phagosomal-lysosomal fusion

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Arthrogryposis, Renal Dysfunction, And Cholestasis	arthrogryposis, renal dysfunction, and cholestasis 1	rs11542638, rs121434385, rs1596358564, rs794726658, rs1596348299, rs1555460030, rs398122407, rs398122408, rs769333468, rs751858602, rs372769808, rs1555459218, rs121434383, rs1555459968, rs121434384	N/A

Show/Hide Unknown Diseases (10)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Coronary artery disease	Coronary artery disease	N/A	N/A	GWAS
Diabetes	Type 2 diabetes	N/A	N/A	GWAS
Hypertension	Hypertension	N/A	N/A	GWAS
Insomnia	Insomnia	N/A	N/A	GWAS
Ischemic Stroke	Ischemic stroke	N/A	N/A	GWAS
Kidney Disease	Chronic kidney disease	N/A	N/A	GWAS
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS
Microcephaly	microcephaly	N/A	N/A	ClinVar
Myocardial Infarction	Myocardial infarction	N/A	N/A	GWAS
Restless Legs Syndrome	Restless legs syndrome	N/A	N/A	GWAS

Show/Hide Text Mining Associations (22)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
AIDS Related Complex	Associate	18853461, 24782640
Arthrogryposis	Associate	16123220, 24415890, 34531360, 35325493, 35761207, 37062417
Arthrogryposis renal dysfunction cholestasis syndrome	Associate	16123220, 18853461, 22753090, 23190456, 24415890, 24782640, 26463206, 26505894, 29624233, 29907094, 35151346, 35325493, 35761207
Blood Platelet Disorders	Associate	18853461
Cholestasis	Associate	24415890, 34531360, 35151346, 35325493, 37062417
Conjunctivitis	Associate	34531360
Deafness	Associate	35151346
Essential Tremor	Associate	36183486
Failure to Thrive	Associate	35151346
Fanconi Syndrome	Associate	29907094, 35151346
Hemorrhage	Associate	18853461, 26505894
Hypertension	Associate	30226566
Hypothyroidism	Associate	34531360
Ichthyosis	Associate	35761207
Jaundice	Associate	35761207
Jaundice Obstructive	Associate	35761207
Kidney Diseases	Associate	24415890, 29907094, 34531360, 35325493, 37062417
Multiple System Atrophy	Associate	35325493
Myocardial Infarction	Associate	30226566
Proteinuria	Associate	34531360
Pruritus	Associate	35761207
Renal Insufficiency Chronic	Associate	30226566

VPS33B (VPS33B late endosome and lysosome associated)