PRUNE1 (prune exopolyphosphatase 1)

Gene

• Entrez ID: 58497
• Gene name: Prune exopolyphosphatase 1
• Gene symbol: PRUNE1
• Synonyms: DRES-17, DRES17, H-PRUNE, HTCD37, NMIHBA, PRUNE
• Chromosome: 1
• Chromosome location: 1q21.3
• Summary: This gene encodes a member of the DHH protein superfamily of phosphoesterases. This protein has been found to function as both a nucleotide phosphodiesterase and an exopolyphosphatase. This protein is believed to stimulate cancer progression and metastase

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs137929776	C>T	Pathogenic	5 prime UTR variant, intron variant, stop gained, coding sequence variant
rs200618384	G>C,T	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained, intron variant, 5 prime UTR variant, missense variant
rs752599948	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, missense variant
rs767769359	G>A,C,T	Pathogenic, likely-pathogenic	Intron variant, missense variant, coding sequence variant, 5 prime UTR variant
rs773618224	G>A	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant, intron variant, synonymous variant
rs886039608	A>G	Pathogenic, likely-pathogenic	Splice acceptor variant, intron variant
rs1057521927	G>A	Likely-pathogenic, pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant, intron variant, non coding transcript variant
rs1085308033	C>A	Pathogenic	5 prime UTR variant, missense variant, intron variant, coding sequence variant
rs1553253812	G>-	Pathogenic	Intron variant, frameshift variant, coding sequence variant, non coding transcript variant
rs1553254265	T>C	Likely-pathogenic	Intron variant, coding sequence variant, missense variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT439887	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT439887	hsa-miR-218-5p	HITS-CLIP	23212916

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004309	Function	Exopolyphosphatase activity	IBA	21873635
GO:0004427	Function	Inorganic diphosphatase activity	IEA
GO:0005515	Function	Protein binding	IPI	10602478
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005829	Component	Cytosol	IDA
GO:0005925	Component	Focal adhesion	IEA
GO:0006798	Process	Polyphosphate catabolic process	IBA	21873635
GO:0015631	Function	Tubulin binding	IDA	28334956
GO:0016311	Process	Dephosphorylation	IEA
GO:0016791	Function	Phosphatase activity	IDA	28334956
GO:0031113	Process	Regulation of microtubule polymerization	IMP	28334956
GO:0046872	Function	Metal ion binding	IEA
GO:0050767	Process	Regulation of neurogenesis	IMP	28334956

Other IDs

• MIM: 617413
• HGNC: 13420
• e!Ensembl: ENSG00000143363

Protein

• UniProt ID: Q86TP1
• Protein name: Exopolyphosphatase PRUNE1 (EC 3.6.1.1) (Drosophila-related expressed sequence 17) (DRES-17) (DRES17) (HTcD37) (Protein prune homolog 1) (hPrune)
• Protein function: Phosphodiesterase (PDE) that has higher activity toward cAMP than cGMP, as substrate. Plays a role in cell proliferation, migration and differentiation, and acts as a negative regulator of NME1. Plays a role in the regulation of neurogenesis (Pu
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01368	DHH	19 → 176	DHH family	Family
  PF02833	DHHA2	216 → 358	DHHA2 domain	Family

• Sequence:

  MEDYLQGCRAALQESRPLHVVLGNEACDLDSTVSALALAFYLAKTTEAEEVFVPVLNIKR
  SELPLRGDIVFFLQKVHIPESILIFRDEIDLHALYQAGQLTLILVDHHILSKSDTALEEA
  VAEVLDHRPIEPKHCPPCHVSVELVGSCATLVTERILQGAPEILDRQTAALLHGTIILDC
  VNMDLKIGKATPKDSKYVEKLEALFPDLPKRNDIFDSLQKAKFDVSGLTTEQMLRKDQKT
  IYRQGVKVAISAIYMDLEAFLQRSNLLADLHAFCQAHSYDVLVAMTIFFNTHNEPVRQLA
  IFCPHVALQTTICEVLERSHSPPLKLTPASSTHPNLHAYLQGNTQVSRKKLLPLLQEALS
  AYFDSMKIPSGQPETADVSREQVDKELDRASNSLISGLSQDEEDPPLPPTPMNSLVDECP
  LDQGLPKLSAEAVFEKCSQISLSQSTTASLSKK

• Sequence length: 453

Pathways

KEGG:

Purine metabolism
Metabolic pathways

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Developmental delay	Profound 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
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
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies	NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, HYPOTONIA, AND VARIABLE BRAIN ANOMALIES	rs886039608, rs1057521927, rs767769359, rs773618224, rs200618384, rs1085308033, rs752599948, rs137929776, rs752940799, rs1574596084	30556349, 28334956, 28211990, 26539891
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085

Unknown
Disease name	Disease term	dbSNP ID	References
Cerebellar atrophy	Cerebellar atrophy
Cerebral cortical atrophy	Cerebral cortical atrophy
Congenital clubfoot	Congenital clubfoot
Hypoplasia of corpus callosum	Hypoplasia of corpus callosum
Macrotia	Macrotia
Neurological syndrome	PRUNE1-related neurological syndrome
Plagiocephaly	Plagiocephaly
Proptosis	Exophthalmos
Spastic tetraparesis	Spastic tetraparesis	rs35077384