USB1 (U6 snRNA biogenesis phosphodiesterase 1)

Gene

• Entrez ID: 79650
• Gene name: U6 snRNA biogenesis phosphodiesterase 1
• Gene symbol: USB1
• Synonyms (NCBI Gene): C16orf57, HVSL1, Mpn1, PN, hMpn1, hUsb1
• Disease Acronyms (UniProt): PN
• Chromosome: 16
• Chromosome location: 16q21
• Summary: This gene encodes a protein with several conserved domains, however, its exact function is not known. Mutations in this gene are associated with poikiloderma with neutropenia (PN), which shows phenotypic overlap with Rothmund-Thomson syndrome (RTS) caused

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs137853970	A>C	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs137853971	A>G	Pathogenic	Intron variant, coding sequence variant, genic downstream transcript variant, missense variant
rs137853972	AGGAACTACAGG>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, splice donor variant
rs771096742	T>A,C	Pathogenic	Coding sequence variant, stop gained, synonymous variant
rs777667891	TCAA>-	Pathogenic	Genic downstream transcript variant, frameshift variant, intron variant, coding sequence variant
rs1249059283	A>C,G	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs1292827495	G>T	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1459714680	C>T	Pathogenic	Genic downstream transcript variant, coding sequence variant, stop gained
rs1555498092	G>A	Pathogenic	Splice acceptor variant
rs1555498117	->C	Pathogenic	Frameshift variant, coding sequence variant
rs1555498120	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555498129	C>T	Pathogenic	Stop gained, coding sequence variant
rs1555498396	A>G	Pathogenic	Intron variant, genic downstream transcript variant, splice acceptor variant
rs1555498399	A>-	Pathogenic	Frameshift variant, intron variant, genic downstream transcript variant, coding sequence variant
rs1555498563	T>G	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant
rs1555498565	A>-	Pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant
rs1555498573	C>T	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant
rs1555498581	G>A	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1597049287	T>C	Likely-pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT028794	hsa-miR-26b-5p	Microarray	19088304
MIRT050173	hsa-miR-26a-5p	CLASH	23622248
MIRT491593	hsa-miR-4524b-3p	PAR-CLIP	23592263
MIRT491591	hsa-miR-6758-5p	PAR-CLIP	23592263
MIRT491592	hsa-miR-6856-5p	PAR-CLIP	23592263
MIRT491590	hsa-miR-3125	PAR-CLIP	23592263
MIRT491589	hsa-miR-3916	PAR-CLIP	23592263
MIRT491588	hsa-miR-6859-5p	PAR-CLIP	23592263
MIRT491587	hsa-miR-4779	PAR-CLIP	23592263
MIRT491586	hsa-miR-4524a-3p	PAR-CLIP	23592263
MIRT491585	hsa-miR-3150b-3p	PAR-CLIP	23592263
MIRT491584	hsa-miR-4784	PAR-CLIP	23592263
MIRT491583	hsa-miR-6077	PAR-CLIP	23592263
MIRT491582	hsa-miR-185-5p	PAR-CLIP	23592263
MIRT491581	hsa-miR-4306	PAR-CLIP	23592263
MIRT491580	hsa-miR-4644	PAR-CLIP	23592263
MIRT491579	hsa-miR-765	PAR-CLIP	23592263
MIRT491577	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT491578	hsa-miR-6825-5p	PAR-CLIP	23592263
MIRT491593	hsa-miR-4524b-3p	PAR-CLIP	23592263
MIRT491591	hsa-miR-6758-5p	PAR-CLIP	23592263
MIRT491592	hsa-miR-6856-5p	PAR-CLIP	23592263
MIRT491590	hsa-miR-3125	PAR-CLIP	23592263
MIRT491589	hsa-miR-3916	PAR-CLIP	23592263
MIRT491588	hsa-miR-6859-5p	PAR-CLIP	23592263
MIRT491587	hsa-miR-4779	PAR-CLIP	23592263
MIRT491586	hsa-miR-4524a-3p	PAR-CLIP	23592263
MIRT491585	hsa-miR-3150b-3p	PAR-CLIP	23592263
MIRT491584	hsa-miR-4784	PAR-CLIP	23592263
MIRT491583	hsa-miR-6077	PAR-CLIP	23592263
MIRT491582	hsa-miR-185-5p	PAR-CLIP	23592263
MIRT491581	hsa-miR-4306	PAR-CLIP	23592263
MIRT491580	hsa-miR-4644	PAR-CLIP	23592263
MIRT491579	hsa-miR-765	PAR-CLIP	23592263
MIRT491577	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT491578	hsa-miR-6825-5p	PAR-CLIP	23592263

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000175	Function	3'-5'-exoribonuclease activity	IBA	21873635
GO:0000175	Function	3'-5'-exoribonuclease activity	IDA	23190533
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	22899009
GO:0005654	Component	Nucleoplasm	IDA
GO:0008380	Process	RNA splicing	IMP	22899009
GO:0034477	Process	U6 snRNA 3'-end processing	IBA	21873635
GO:0034477	Process	U6 snRNA 3'-end processing	IMP	22899009
GO:0045171	Component	Intercellular bridge	IDA
GO:0090503	Process	RNA phosphodiester bond hydrolysis, exonucleolytic	IEA
GO:1990838	Function	Poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends	IEA

Other IDs

• MIM: 613276
• HGNC: 25792
• e!Ensembl: ENSG00000103005

Protein

• UniProt ID: Q9BQ65
• Protein name: U6 snRNA phosphodiesterase 1 (hUsb1) (3'-5' RNA exonuclease USB1) (EC 4.6.1.-) (Mutated in poikiloderma with neutropenia protein 1) (Mutated in PN protein 1) (hMpn1)
• Protein function: 3'-5' RNA exonuclease that trims the 3' end of oligo(U) and oligo(A) tracts of the pre-U6 small nuclear RNA (snRNA) molecule, leading to the formation of a mature U6 snRNA 3' end-terminated with a 2',3'-cyclic phosphate (PubMed:22899009, PubMed:
• PDB: 4H7W, 5V1M, 6D2Z, 6D30, 6D31
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF09749	HVSL	43 → 263	Uncharacterised conserved protein	Family

• Sequence:

  MSAAPLVGYSSSGSEDESEDGMRTRPGDGSHRRGQSPLPRQRFPVPDSVLNMFPGTEEGP
  EDDSTKHGGRVRTFPHERGNWATHVYVPYEAKEEFLDLLDVLLPHAQTYVPRLVRMKVFH
  LSLSQSVVLRHHWILPFVQALKARMTSFHRFFFTANQVKIYTNQEKTRTFIGLEVTSGHA
  QFLDLVSEVDRVMEEFNLTTFYQDPSFHLSLAWCVGDARLQLEGQCLQELQAIVDGFEDA
  EVLLRVHTEQVRCKSGNKFFSMPLK

• Sequence length: 265

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Anemia	Anemia	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Cataract	Cataract	rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322, rs121917775, rs121917735, rs121917736, rs137853199, rs137853200, rs121917867, rs121917869, rs121913555, rs104893736, rs121909595, rs121909596, rs121909597, rs28931605, rs121909598, rs104893618, rs1695062782, rs74315486, rs74315487, rs74315490, rs74315489, rs745938679, rs1566402656, rs74315439, rs74315441, rs121912973, rs121917823, rs1593332981, rs121917825, rs121917827, rs113994108, rs387906963, rs387906964, rs1240503246, rs387906965, rs387906966, rs750207077, rs387907336, rs387907337, rs387907342, rs140332366, rs397514703, rs398122937, rs398122378, rs398122392, rs398122944, rs137853924, rs398122947, rs397515623, rs397515624, rs397515625, rs397515626, rs398122948, rs587778872, rs398123066, rs587777601, rs370424081, rs786205221, rs786205222, rs864309684, rs864309688, rs864309701, rs864309689, rs864309690, rs864309681, rs864309686, rs864309696, rs864309693, rs864309687, rs864309691, rs864309692, rs864309695, rs864309678, rs864309685, rs864309700, rs864309698, rs864309683, rs864309682, rs864309679, rs111534978, rs864309680, rs864309702, rs864622780, rs756898971, rs869312732, rs775038545, rs878852983, rs1114167312, rs1114167313, rs1114167314, rs1114167315, rs1114167307, rs886041410, rs886041412, rs1057518738, rs1057517926, rs1057518878, rs1057519616, rs12799308, rs1064793935, rs1064797219, rs1085307126, rs1085307127, rs765628635, rs1114167427, rs1114167433, rs1554744860, rs1554743428, rs747093432, rs1411557416, rs1555179713, rs1481963503, rs1555549755, rs1456161420, rs1555547008, rs1555889308, rs1555888762, rs766522434, rs1264025914, rs1553585262, rs1567671947, rs1337897299, rs764945940, rs1307969607, rs949335475, rs1184095219, rs776129797, rs1569203234, rs1567668570, rs749141857, rs764098604, rs1184398243, rs1578956689, rs1568480054, rs1564745688, rs1564722302, rs1564723150, rs1571175950, rs1569602837, rs1576552712, rs1575369255, rs981126461, rs1570403798, rs200557771, rs1477743112, rs1651879427, rs1651881222, rs1651919374, rs2024441691, rs148284531, rs1246080692
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
Diabetes mellitus	Diabetes Mellitus	rs587776515, rs61730328, rs606231121, rs606231122, rs79020217, rs77625743, rs78378398, rs606231123, rs1362648752, rs104893649, rs80356624, rs80356616, rs80356625, rs80356611, rs104894237, rs80356613, rs387906407, rs151344623, rs28938469, rs28936371, rs137852672, rs80356637, rs80356642, rs80356653, rs137852673, rs137852674, rs80356634, rs80356651, rs193929360, rs137853334, rs137853335, rs137853336, rs1600731198, rs137853338, rs121964882, rs121964883, rs387906511, rs121964884, rs121964885, rs2147483647, rs387906512, rs121964887, rs121964888, rs121964889, rs121964890, rs121964891, rs28934878, rs74315383, rs121964893, rs886037620, rs886037621, rs121434593, rs121913150, rs587776825, rs137853236, rs2135842335, rs137853237, rs137853238, rs2135818776, rs1566092470, rs1463923467, rs137853243, rs137853244, rs2135839114, rs137853245, rs2135847417, rs121918407, rs104894005, rs104894006, rs80356655, rs104894008, rs104894009, rs104894010, rs104894011, rs80356654, rs104894016, rs193929376, rs193929374, rs193929375, rs193929373, rs80356669, rs80356664, rs193929366, rs1048095, rs193929355, rs193929356, rs1259467443, rs104893642, rs387906777, rs193922396, rs193922400, rs193922401, rs137852676, rs193922407, rs193922638, rs193922257, rs193922258, rs193922259, rs193922260, rs193922261, rs193922262, rs193922263, rs193922264, rs193922265, rs193922268, rs193921338, rs193922269, rs193922272, rs193922273, rs193922275, rs193922278, rs193922279, rs193922280, rs193922281, rs193922282, rs193922283, rs193922284, rs193922286, rs193922287, rs193922289, rs193922291, rs193922295, rs193922297, rs193922300, rs193922302, rs193922303, rs193922308, rs193922313, rs193922314, rs144723656, rs193922315, rs193922316, rs193922317, rs148311934, rs193922319, rs193922320, rs193922326, rs193922329, rs193922330, rs193922331, rs193922335, rs193922336, rs193922338, rs193922340, rs193922341, rs193922471, rs193922475, rs193922476, rs193922479, rs80356663, rs193922355, rs193922356, rs193922576, rs193922578, rs193922582, rs193922588, rs193922592, rs193922594, rs193922596, rs386134267, rs193922598, rs193922599, rs193922600, rs193922604, rs193922605, rs397514580, rs397515519, rs267601516, rs587780343, rs587780345, rs587780346, rs587780347, rs587780357, rs148954387, rs587783672, rs587783669, rs786204676, rs794727236, rs151344624, rs794727775, rs794727839, rs199946797, rs869320673, rs796065047, rs759072800, rs797045595, rs797045209, rs797045207, rs797045213, rs863225280, rs149703259, rs864321656, rs139964066, rs777870079, rs878853246, rs769268803, rs886039380, rs886041392, rs886041391, rs886042610, rs143064649, rs1057516192, rs746480424, rs1057516281, rs576684889, rs754728827, rs1057520291, rs1057520779, rs893256143, rs1057520504, rs1057524790, rs1057524902, rs1057524904, rs1057524905, rs764232985, rs1064793998, rs1064794268, rs769086289, rs369429452, rs1085307913, rs1131691416, rs765432081, rs1131692182, rs748749585, rs1554335441, rs762263694, rs1312678560, rs767565869, rs1375656631, rs1554335391, rs1360415315, rs1554335616, rs1554335752, rs1554909277, rs769518471, rs757171524, rs768951263, rs762703502, rs1555212248, rs1555212359, rs1555813319, rs1555816654, rs371977235, rs1415041911, rs1554334894, rs1260178539, rs1554335421, rs1555211904, rs779184183, rs1554335564, rs200670692, rs1400535021, rs1554334872, rs1555212749, rs1553876668, rs1553878211, rs954727530, rs1554924035, rs372307320, rs925231098, rs1554913069, rs1554933565, rs766431403, rs746714109, rs751279984, rs770664202, rs1008906426, rs758844607, rs1554924540, rs1566092307, rs753998395, rs1565885935, rs1167124132, rs1376796469, rs556436603, rs1562715657, rs1486280029, rs1564869850, rs755259997, rs769569410, rs1172328722, rs1286294151, rs1375557127, rs1568731279, rs1562715426, rs556581174, rs1564865302, rs1565886545, rs1568724014, rs1392795567, rs781260712, rs1562719705, rs1382448285, rs1564977373, rs750586210, rs1598842892, rs1583592247, rs780612692, rs1593060859, rs1476637197, rs751279776, rs1593060890, rs1191912908, rs1167675604, rs1583601110, rs1593058932, rs778611627, rs753296261
Dyskeratosis congenita	Dyskeratosis Congenita, Dyskeratosis congenita	rs121908092, rs121908089, rs121908090, rs121908091, rs121918543, rs121918544, rs121918545, rs1553915517, rs199422284, rs199476393, rs199422277, rs199422270, rs137854489, rs121912288, rs121912304, rs121918665, rs121918666, rs199422294, rs199422263, rs281865549, rs199473674, rs202138550, rs387907080, rs373905859, rs199473677, rs199473676, rs199473682, rs199473673, rs387907153, rs387907154, rs387907249, rs863223324, rs199422311, rs199422315, rs199422314, rs199422316, rs121912289, rs121912297, rs1554041299, rs199422297, rs199422298, rs199422305, rs199422255, rs199422269, rs199422274, rs199422278, rs199422257, rs199422262, rs199422264, rs199422266, rs199422267, rs199473679, rs397514660, rs281865547, rs201540674, rs370343781, rs398123017, rs398123048, rs398123051, rs373740199, rs398123052, rs786200999, rs756132866, rs786201001, rs797045144, rs776744306, rs863225129, rs886039438, rs1553915577, rs1553915591, rs745590324, rs942538351, rs1555512179, rs1444923772, rs1555899096, rs1555903332, rs1555814400, rs1553915580, rs770066110, rs1553915590, rs80224512, rs1555899111, rs200609323, rs1196342305, rs1285014916, rs773025155, rs895722334, rs1555811742, rs1555812228, rs1555812480, rs1421904176, rs1555811386, rs1555813123, rs1161373315, rs1555901832, rs961593162, rs1555813144, rs1415449695, rs1555814334, rs980695424, rs778734749, rs1555901000, rs780546933, rs1263776141, rs377024903, rs1555811966, rs1555812178, rs752833281, rs1555812834, rs1555814044, rs377461417, rs1567599296, rs764019241, rs1449687529, rs1569558474, rs767991627, rs1306444586, rs1596812454, rs915854031, rs1597422298, rs938938578, rs1597374251, rs745467709, rs1461036243, rs62637613, rs769617113, rs773120259, rs372031509	22160078, 20817924, 20004881
Liver failure	Liver Failure	rs118203990, rs118203991, rs118203992, rs387907022, rs201861847, rs796065037, rs759315662, rs368196005, rs796052121, rs369437593, rs367683258, rs766314948, rs368085185, rs770446752, rs753039116, rs776797592, rs1490906786, rs1562849964, rs759960319, rs776597537, rs375350359, rs1573008071, rs1601977105, rs1174791046, rs1019313682
Lymphoma	Lymphoma	rs11540652, rs1592119138, rs1592123162, rs1599367044
Neutropenia	Neutropenia	rs879253882
Osteoporosis	Osteoporosis	rs72658152, rs72667023, rs587776916, rs72656370, rs768615287
Palmoplantar keratoderma	Keratoderma, Palmoplantar	rs59616921, rs1568039793, rs746488412, rs200564757, rs1567027297, rs781596375, rs1567027610, rs398123054, rs398123055, rs398123056, rs398123057, rs398122949, rs398122950, rs397515639, rs398122951, rs397515640, rs397515641, rs142859678, rs797044479, rs577442939, rs672601344, rs568609861, rs1057518846, rs1182196436, rs1567037561
Periodontitis	Periodontitis	rs28937571, rs104894211, rs587777534
Poikiloderma with neutropenia	Poikiloderma with Neutropenia, Poikiloderma with neutropenia	rs137853970, rs137853972, rs137853971, rs786205051, rs137853973, rs1555498399, rs1555498565, rs1555498573, rs1249059283, rs1459714680, rs1292827495, rs759761915, rs1555498092, rs1555498129, rs777667891, rs1555498120, rs1597049287	25044170, 20004881, 21271650, 20503306, 20817924, 21872685, 20618321
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085

Unknown
Disease term	Disease name	Evidence	References	Source
Cirrhosis	Cirrhosis			ClinVar
Otitis media	Recurrent otitis media			ClinVar
Dyskeratosis Congenita	dyskeratosis congenita			GenCC

Associations from Text Mining
Disease Name	Relationship Type	References
Abnormalities Drug Induced	Associate	31522452
Breast Neoplasms	Associate	26872609
Carcinogenesis	Associate	26872609
Cholangiocarcinoma	Associate	32020235
Dubowitz syndrome	Associate	27612988
Dyskeratosis Congenita	Associate	20817924, 22899009, 27612988
Dystonic Disorders	Associate	26306619
Ectodermal Dysplasia	Associate	27612988
Ectrodactyly	Associate	26546903
Genetic Diseases Inborn	Associate	23190533
Growth Disorders	Associate	27612988
Leukemia Myeloid Acute	Associate	37164308
Lung Diseases	Associate	26273833
Myelodysplastic Syndromes	Associate	26306619
Neoplasms	Inhibit	24887023
Neoplasms	Associate	26306619, 26872609, 27028305
Neural Tube Defects	Associate	26306619
Neutropenia	Associate	20817924, 22899009, 26213367, 26987923, 27612988, 35522049
Osteosarcoma	Associate	27028305
Pneumonia	Associate	36217141
Poikiloderma with Neutropenia	Associate	20004881, 20817924, 21271650, 22269211, 22899009, 23022480, 23190533, 26213367, 26306619, 26546903, 26987923, 30215753, 31522452
Rett Syndrome	Associate	20817924
Rothmund Thomson Syndrome	Associate	20004881, 20817924, 22899009, 26213367, 27612988, 35522049
Stomach Neoplasms	Inhibit	24887023