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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	63894
Gene name	VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog
Gene symbol	VIPAS39
Synonyms (NCBI Gene)	C14orf133SPE-39SPE39VIPARVPS16BhSPE-39
Chromosome	14
Chromosome location	14q24.3
Summary	This gene encodes a protein involved in the sorting of lysosomal proteins. Mutations in this gene are associated with ARCS2 (arthrogryposis, renal dysfunction, and cholestasis-2). Alternative splicing results in multiple transcript variants.[provided by R

Show/Hide all (23)

SNP ID	Visualize variation	Clinical significance	Consequence
rs112217896	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs138544284	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs144120903	G>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant
rs145373891	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs145453157	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Synonymous variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs147303718	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant
rs148623263	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, intron variant, non coding transcript variant
rs188105111	A>G	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, genic downstream transcript variant, coding sequence variant, downstream transcript variant, non coding transcript variant
rs200370925	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs267607171	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs267607172	A>C	Pathogenic	Non coding transcript variant, initiator codon variant, missense variant
rs267607173	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, stop gained
rs371371767	G>A,C	Conflicting-interpretations-of-pathogenicity	Intron variant
rs371762531	T>C	Conflicting-interpretations-of-pathogenicity	Intron variant
rs747749610	G>A	Likely-pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs794726653	GTTCT>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs988006454	G>A	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, intron variant
rs1555364979	C>T	Pathogenic	Stop gained, coding sequence variant, downstream transcript variant, non coding transcript variant, genic downstream transcript variant
rs1555366438	T>C	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1566731055	A>G	Likely-pathogenic	Splice donor variant
rs1594895847	C>T	Pathogenic	Splice donor variant
rs1594910243	->AGTGTCCTC	Likely-pathogenic	Inframe insertion, non coding transcript variant, coding sequence variant
rs1594929571	T>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant

Show/Hide all (1)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029282	hsa-miR-26b-5p	Microarray	19088304

Show/Hide all (35)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	16189514, 19109425, 20190753, 22677173, 23901104, 23918659, 25783203, 26871637, 28017832, 29778605, 32296183
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	20190753
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IDA	23918659
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IDA	19109425
GO:0005769	Component	Early endosome	IEA
GO:0005770	Component	Late endosome	IDA	19109425
GO:0005770	Component	Late endosome	IEA
GO:0005794	Component	Golgi apparatus	IDA	27435297
GO:0006886	Process	Intracellular protein transport	IBA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006886	Process	Intracellular protein transport	IMP	19109425
GO:0007034	Process	Vacuolar transport	IBA
GO:0007283	Process	Spermatogenesis	IEA
GO:0008333	Process	Endosome to lysosome transport	IMP	25783203
GO:0008333	Process	Endosome to lysosome transport	IMP	19109425
GO:0015031	Process	Protein transport	IEA
GO:0017185	Process	Peptidyl-lysine hydroxylation	IMP	27435297
GO:0030154	Process	Cell differentiation	IEA
GO:0030199	Process	Collagen fibril organization	IEA
GO:0030897	Component	HOPS complex	IDA	25783203
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0032963	Process	Collagen metabolic process	IEA
GO:0032963	Process	Collagen metabolic process	IMP	27435297
GO:0043687	Process	Post-translational protein modification	IEA
GO:0044877	Function	Protein-containing complex binding	IDA	19109425
GO:0055037	Component	Recycling endosome	IDA	19109425
GO:0055037	Component	Recycling endosome	IEA
GO:0090385	Process	Phagosome-lysosome fusion	NAS	27555442
GO:0097352	Process	Autophagosome maturation	IMP	25783203
GO:0099023	Component	Vesicle tethering complex	IEA
GO:0099023	Component	Vesicle tethering complex	IPI	23918659

MIM	HGNC	e!Ensembl
613401	20347	ENSG00000151445

Q9H9C1

Protein name

Spermatogenesis-defective protein 39 homolog (hSPE-39) (VPS33B-interacting protein in apical-basolateral polarity regulator) (VPS33B-interacting protein in polarity and apical restriction)

Protein function

Proposed to be involved in endosomal maturation implicating in part VPS33B. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical RAB11A-dependent recycling pathway and in the maintenance of the apical-basolateral polarit

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04840	Vps16_C	164 → 305	Vps16, C-terminal region	Family

Sequence

MNRTKGDEEEYWNSSKFKAFTFDDEDDELSQLKESKRAVNSLRDFVDDDDDDDLERVSWS
GEPVGSISWSIRETAGNSGSTHEGREQLKSRNSFSSYAQLPKPTSTYSLSSFFRGRTRPG
SFQSLSDALSDTPAKSYAPELGRPKGEYRDYSNDWSPSDTVRRLRKGKVCSLERFRSLQD
KLQLLEEAVSMHDGNVITAVLIFLKRTLSKEILFRELEVRQVALRHLIHFLKEIGDQKLL
LDLFRFLDRTEELALSHYREHLNIQDPDKRKEFLKTCVGLPFSAEDSAHIQDHYTLLERQ
IIIEANDRHLESAGQTEIFRKHPRKASILNMPLVTTLFYSCFYHYTEAEGTFSSPVNLKK
TFKIPDKQYVLTALAARAKLRAWNDVDALFTTKNWLGYTKKRAPIGFHRVVEILHKNNAP
VQILQEYVNLVEDVDTKLNLATKFKCHDVVIDTYRDLKDRQQLLAYRSKVDKGSAEEEKI
DALLSSSQIRWKN

Sequence length

493

Interactions

View interactions

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
Arthrogryposis with renal dysfunction and cholestasis syndrome	Pathogenic	rs755556421	RCV004017979	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Arthrogryposis, renal dysfunction, and cholestasis 1	Pathogenic	rs1594929571, rs1594895847	RCV000790402 RCV000790403	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Arthrogryposis, renal dysfunction, and cholestasis 2	Pathogenic; Likely pathogenic	rs200779594, rs267607173, rs794726653, rs200370925, rs267607171, rs267607172, rs2139895315, rs778181495, rs755556421, rs2503151300, rs747670551, rs747749610, rs1555364979, rs1555366438, rs1594910243	RCV005005927 RCV000000131 RCV000000132 RCV000000133 RCV000000134 View all (10 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (9)

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.
ARTHROGRYPOSIS RENAL DYSFUNCTION CHOLESTASIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ARTHROGRYPOSIS-RENAL DYSFUNCTION-CHOLESTASIS SYNDROME	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VIPAS39-related disorder	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (30)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Arthrogryposis	Arthrogryposis multiplex congenita	BEFREE	22753090, 26463206, 26808426		★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthrogryposis	Arthrogryposis multiplex congenita	GENOMICS_ENGLAND_DG	26808426, 27604308		★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthrogryposis	Arthrogryposis	Pubtator	26808426, 35325493, 37062417	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthrogryposis	Arthrogryposis multiplex congenita	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthrogryposis renal dysfunction cholestasis syndrome	Arthrogryposis-renal dysfunction-cholestasis syndrome	Pubtator	22753090, 23002115, 24782640, 26463206, 29907094, 35151346, 35325493, 35761207, 37202112	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Arthrogryposis, renal dysfunction, and cholestasis 1	Arthrogryposis, Renal Dysfunction, And Cholestasis	BEFREE	20190753, 22753090, 23002115, 24782640, 24917129, 25947942, 26463206, 26971401, 28277061, 29409756, 29907094		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Arthrogryposis, renal dysfunction, and cholestasis 1	Arthrogryposis, Renal Dysfunction, And Cholestasis	CTD_human_DG	20190753		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Arthrogryposis, renal dysfunction, and cholestasis 1	Arthrogryposis, Renal Dysfunction, And Cholestasis	ORPHANET_DG	25239142		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Arthrogryposis, renal dysfunction, and cholestasis 1	Arthrogryposis, Renal Dysfunction, And Cholestasis	GENOMICS_ENGLAND_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2	Arthrogryposis, Renal Dysfunction, And Cholestasis	GENOMICS_ENGLAND_DG	20190753		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2	Arthrogryposis, Renal Dysfunction, And Cholestasis	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Arthrogryposis-renal dysfunction-cholestasis syndrome	Arthrogryposis, Renal Dysfunction, And Cholestasis	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Blood Coagulation Disorders	Blood Coagulation Disorders	BEFREE	25947942		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholestasis	Cholestasis	BEFREE	31479177		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholestasis	Cholelithiasis	Pubtator	35325493, 37062417	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholestasis Intrahepatic	Intrahepatic cholestasis	Pubtator	26808426	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholestatic liver disease	Cholestatic liver disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Conjugated hyperbilirubinemia	Conjugated hyperbilirubinemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Fanconi Syndrome	Fanconi syndrome	Pubtator	26808426	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	26808426	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ichthyoses	Ichthyosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intrahepatic Cholestasis	Intrahepatic Cholestasis	BEFREE	26808426		★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	35325493, 37062417	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple System Atrophy	Multiple system atrophy	Pubtator	35325493	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrocalcinosis	Nephrocalcinosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Right Ventricular Hypertrophy	Ventricular hypertrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

VIPAS39 (VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog)