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

Gene

• Entrez ID: 63894
• Gene name: VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog
• Gene symbol: VIPAS39
• Synonyms: C14orf133, SPE-39, SPE39, VIPAR, VPS16B, hSPE-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

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	16189514, 19109425, 20190753, 22677173, 23901104, 23918659, 25783203, 26871637, 28017832, 32296183
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005737	Component	Cytoplasm	IDA	20190753
GO:0005769	Component	Early endosome	IDA	19109425
GO:0005770	Component	Late endosome	IDA	19109425
GO:0005794	Component	Golgi apparatus	IDA	27435297
GO:0006886	Process	Intracellular protein transport	IBA	21873635
GO:0006886	Process	Intracellular protein transport	IMP	19109425
GO:0007034	Process	Vacuolar transport	IBA	21873635
GO:0007283	Process	Spermatogenesis	IEA
GO:0008333	Process	Endosome to lysosome transport	IMP	19109425
GO:0008333	Process	Endosome to lysosome transport	IMP	25783203
GO:0017185	Process	Peptidyl-lysine hydroxylation	IMP	27435297
GO:0030154	Process	Cell differentiation	IEA
GO:0030897	Component	HOPS complex	IDA	25783203
GO:0032963	Process	Collagen metabolic process	IMP	27435297
GO:0044877	Function	Protein-containing complex binding	IDA	19109425
GO:0055037	Component	Recycling endosome	IDA	19109425
GO:0097352	Process	Autophagosome maturation	IMP	25783203

Other IDs

• MIM: 613401
• HGNC: 20347
• e!Ensembl: ENSG00000151445

Protein

• UniProt ID: 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

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Arthrogryposis multiplex congenita	Arthrogryposis	rs1586285494, rs80358233, rs137853305, rs1559154278, rs398124167, rs398124172, rs587780399, rs786204576, rs786204430, rs769345284, rs749355583, rs793888524, rs793888525, rs878854368, rs555445835, rs758105619, rs886041851, rs794727136, rs755239192, rs760715690, rs773952935, rs112610938, rs1057516676, rs1057516996, rs780022652, rs1057517399, rs1057517360, rs1057518353, rs1057517977, rs1064796311, rs779232987, rs775997446, rs1064797093, rs1064797094, rs1064797095, rs755500591, rs754272530, rs758247804, rs200731870, rs747179265, rs1553740233, rs776569219, rs375628303, rs775631800, rs781667543, rs1553548666, rs928945364, rs763364977, rs1458048713, rs1553883480, rs1472403020, rs1336053002, rs202048855, rs1197561990, rs755531536, rs1554112524, rs762133567, rs1553555882, rs934111355, rs1255744452, rs1366269616, rs1555734932, rs1553548207, rs752582527, rs1257495033, rs113525641, rs755863625, rs374929094, rs539819851, rs1366853918, rs1218073575, rs1553537512, rs1553552384, rs747564597, rs776059611, rs756726488, rs1357811155, rs1553939600, rs772009599, rs1255445731, rs1011425121, rs1553561697, rs1553551748, rs1553552413, rs760935667, rs1553603400, rs1302373559, rs1389892619, rs1553710982, rs757157808, rs1180339426, rs761964375, rs1235589246, rs1443738549, rs1553934586, rs1553934597, rs1553603437, rs749452641, rs1553904694, rs754369875, rs112517981, rs774495973, rs1428597732, rs746999970, rs113091511, rs1553603958, rs1553469502, rs770797137, rs1553608621, rs1159756073, rs776167256, rs778593702, rs1553601066, rs1553689774, rs760768475, rs1559296376, rs201636991, rs1559039815, rs748922882, rs772366030, rs1207534366, rs1259297878, rs762780413, rs1559360386, rs1559940778, rs760200697, rs1344099907, rs750900690, rs1559168230, rs746177326, rs761067911, rs1323364980, rs537560378, rs1319778592, rs1340063197, rs1577833924, rs750585238, rs1600470099, rs1575714905, rs1576203853, rs779909544, rs760124743, rs2096362304, rs1212374733, rs1490309743, rs767709270, rs1374971806, rs2096491549, rs2097886912, rs2099021112, rs2097758221, rs1474341248, rs925947627	26808426, 27604308
Arthrogryposis, renal dysfunction, and cholestasis	Arthrogryposis, renal dysfunction, and cholestasis 1, ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2, Arthrogryposis-renal dysfunction-cholestasis syndrome	rs267607173, rs794726653, rs200370925, rs267607171, rs267607172, rs121434383, rs121434384, rs121434385, rs794726658, rs1555460030, rs398122407, rs398122408, rs864622006, rs769333468, rs751858602, rs372769808, rs747749610, rs1555364979, rs1555366438, rs1555459218, rs1555459968, rs11542638, rs1594910243, rs1596358564, rs1594929571, rs1594895847, rs1596348299	20190753, 25239142, 20190753
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Ichthyosis	Ichthyoses	rs199766569, rs587776996, rs587777262, rs863223405, rs370031870, rs1569044747, rs200806519
Kidney disease	Kidney Diseases	rs74315342, rs749740335, rs757649673, rs112417755, rs35138315
Microcephaly	Microcephaly	rs397704721, rs267607176, rs267607177, rs397704725, rs267606717, rs267606718, rs199422202, rs121434311, rs199422203, rs199422126, rs387906274, rs121434305, rs199422125, rs199422135, rs189678019, rs199422184, rs137852994, rs137852995, rs137852996, rs137852997, rs145489194, rs80338860, rs137852494, rs121918609, rs199422207, rs199422206, rs29001566, rs864321658, rs199422138, rs199422139, rs199422141, rs199422144, rs199422147, rs199422151, rs199422152, rs199422153, rs199422157, rs199422159, rs199422160, rs199422161, rs140602858, rs199422164, rs199422165, rs148294838, rs199422134, rs199422168, rs199422172, rs199422173, rs199422131, rs199422177, rs199422180, rs199422185, rs199422186, rs199422187, rs143931757, rs199422189, rs199422192, rs199422194, rs199422195, rs199422196, rs199422197, rs199422199, rs753597039, rs1488084787, rs387906961, rs755862917, rs387907082, rs587776899, rs387907083, rs587776900, rs587776901, rs387907084, rs863223322, rs764201220, rs202247811, rs763915472, rs587776986, rs587777036, rs398122971, rs374351172, rs373278668, rs398122976, rs121909123, rs587783393, rs730882076, rs587783211, rs144716013, rs606231255, rs587783215, rs587783216, rs587783220, rs587783221, rs587783225, rs587783227, rs587783228, rs587783230, rs587783238, rs587783239, rs587783240, rs587783245, rs587783247, rs587783248, rs587783258, rs587783259, rs587783263, rs587783265, rs587783268, rs587783269, rs587783272, rs587783275, rs587783277, rs587783278, rs587783280, rs587783282, rs587783283, rs587783285, rs587783287, rs587783288, rs587783289, rs587783292, rs587783295, rs587784452, rs587783741, rs587783735, rs587783392, rs587783390, rs587783387, rs587783410, rs202058504, rs587783423, rs587783421, rs587783414, rs587784553, rs587784558, rs587784546, rs587784549, rs587784554, rs587784412, rs876661307, rs869025200, rs747831095, rs748529285, rs797045316, rs797045315, rs797045314, rs759632528, rs797045313, rs797045311, rs754282058, rs797045441, rs797045454, rs797045430, rs869312853, rs797046109, rs767399782, rs863225127, rs863225464, rs863225465, rs780270096, rs864321621, rs864321620, rs775277800, rs879253817, rs869312824, rs761447719, rs753406334, rs147622433, rs199422137, rs879255522, rs879255524, rs879255523, rs886037892, rs886037893, rs886037894, rs886037895, rs199422169, rs886041709, rs886041282, rs138228629, rs759188041, rs769688376, rs1057517688, rs1057519087, rs1057518268, rs933106143, rs201362977, rs754909135, rs1057520873, rs1060499758, rs1060499757, rs199422146, rs748016594, rs1085307120, rs763715733, rs1064795945, rs763800571, rs1554728351, rs1553227021, rs555866170, rs1553895368, rs1334947797, rs769818500, rs1321892596, rs1553227645, rs1404276011, rs1553228275, rs1554471681, rs1554496609, rs1555420891, rs1555418825, rs587784548, rs1555723585, rs199736219, rs745997770, rs765275884, rs1553924800, rs1554730137, rs1229568621, rs1482100822, rs979186313, rs758157294, rs1555294652, rs1555299107, rs1553264033, rs1553259539, rs1553254322, rs1553259528, rs981349334, rs1553264036, rs1553253022, rs754267846, rs776034810, rs1342429887, rs752140135, rs1006898944, rs571640983, rs1477524771, rs763909256, rs199910503, rs1553223496, rs759663956, rs1553446603, rs1555139372, rs1555143325, rs1350194762, rs1555141158, rs1553225179, rs769481947, rs769364943, rs748011724, rs1334301723, rs746341112, rs149225624, rs765113367, rs1567024512, rs142865061, rs772050241, rs201721894, rs1557966012, rs1379578836, rs1568334868, rs1185537869, rs1602333390, rs1163303148, rs774338373, rs770540184, rs1571600045, rs1571601267, rs1571602991, rs1588472215, rs1599841026, rs1558328287, rs1571600860, rs1571596976, rs1309880692, rs1435239428, rs1588634016, rs1751797979, rs1810830776, rs1815354949, rs1949984655, rs886039658, rs1943461045, rs777711720, rs2031759596, rs1555710223, rs1221031683, rs774069989, rs2058919680, rs1170413397, rs1213710245, rs1599851667, rs1599760058, rs1971033478, rs746967357
Ventricular septal defect	Ventricular Septal Defects	rs104894073, rs387906775

Unknown
Disease name	Disease term	dbSNP ID	References
Cholestatic liver disease	Cholestatic liver disease
Conjugated hyperbilirubinemia	Conjugated hyperbilirubinemia
Nephrocalcinosis	Nephrocalcinosis
Ventricular hypertrophy	Right Ventricular Hypertrophy