ALG3 (ALG3 alpha-1,3- mannosyltransferase)

Gene

• Entrez ID: 10195
• Gene name: ALG3 alpha-1,3- mannosyltransferase
• Gene symbol: ALG3
• Synonyms (NCBI Gene): CDG1D, CDGS4, CDGS6, D16Ertd36e, NOT56L, Not56, not
• Disease Acronyms (UniProt): CDG1D
• Chromosome: 3
• Chromosome location: 3q27.1
• Summary: This gene encodes a member of the ALG3 family. The encoded protein catalyses the addition of the first dol-P-Man derived mannose in an alpha 1,3 linkage to Man5GlcNAc2-PP-Dol. Defects in this gene have been associated with congenital disorder of glycosyla

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs2233466	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs28940588	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103236	C>A,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs119103237	A>G	Pathogenic	Non coding transcript variant, coding sequence variant, 5 prime UTR variant, intron variant, missense variant
rs119103238	A>G,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs186946267	C>G,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs367679074	C>T	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs370434427	C>A,G,T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs748878963	C>A	Likely-pathogenic	Splice donor variant
rs1028791709	T>C	Likely-pathogenic	Missense variant, 5 prime UTR variant, intron variant, non coding transcript variant, coding sequence variant
rs1085307980	A>G	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1085307981	T>C	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1553827968	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1560162116	T>C	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1560164682	T>C	Likely-pathogenic	Intron variant
rs1577105039	T>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT005225	hsa-let-7b-5p	pSILAC	18668040
MIRT005258	hsa-miR-16-5p	pSILAC	18668040
MIRT023511	hsa-miR-1-3p	Proteomics	18668040
MIRT025687	hsa-miR-7-5p	Microarray	19073608
MIRT027484	hsa-miR-98-5p	Microarray	19088304
MIRT028778	hsa-miR-26b-5p	Microarray	19088304
MIRT005258	hsa-miR-16-5p	Proteomics;Other	18668040
MIRT005258	hsa-miR-16-5p	Microarray	21199864
MIRT005225	hsa-let-7b-5p	Proteomics;Other	18668040
MIRT048444	hsa-miR-100-5p	CLASH	23622248
MIRT046832	hsa-miR-222-3p	CLASH	23622248
MIRT778540	hsa-miR-1200	CLIP-seq
MIRT778541	hsa-miR-3126-5p	CLIP-seq
MIRT778542	hsa-miR-3132	CLIP-seq
MIRT778543	hsa-miR-3153	CLIP-seq
MIRT778544	hsa-miR-3529	CLIP-seq
MIRT778545	hsa-miR-379	CLIP-seq
MIRT778546	hsa-miR-3936	CLIP-seq
MIRT778547	hsa-miR-4324	CLIP-seq
MIRT778548	hsa-miR-4419a	CLIP-seq
MIRT778549	hsa-miR-4436b-3p	CLIP-seq
MIRT778550	hsa-miR-4510	CLIP-seq
MIRT778551	hsa-miR-4726-3p	CLIP-seq
MIRT778552	hsa-miR-510	CLIP-seq
MIRT778553	hsa-miR-544b	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000033	Function	Alpha-1,3-mannosyltransferase activity	IDA	10581255
GO:0000033	Function	Alpha-1,3-mannosyltransferase activity	TAS
GO:0005515	Function	Protein binding	IPI	21516116, 25910212, 29547901, 31515488, 32296183
GO:0005783	Component	Endoplasmic reticulum	IBA	21873635
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	10581255
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006486	Process	Protein glycosylation	IBA	21873635
GO:0006486	Process	Protein glycosylation	NAS	10581255
GO:0006488	Process	Dolichol-linked oligosaccharide biosynthetic process	TAS
GO:0016021	Component	Integral component of membrane	IEA
GO:0052925	Function	Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity	IBA	21873635
GO:0097502	Process	Mannosylation	IEA

Other IDs

• MIM: 608750
• HGNC: 23056
• e!Ensembl: ENSG00000214160

Protein

• UniProt ID: Q92685
• Protein name: Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase (EC 2.4.1.258) (Asparagine-linked glycosylation protein 3 homolog) (Dol-P-Man-dependent alpha(1-3)-mannosyltransferase) (Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase) (Dolich
• Protein function: Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase that operates in the biosynthetic pathway of dolichol-linked oligosaccharides, the glycan precursors employed in protein asparagine (N)-glycosylation. The assembly of dolichol-linked
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05208	ALG3	47 → 406	ALG3 protein	Family

• Sequence:

  MAAGLRKRGRSGSAAQAEGLCKQWLQRAWQERRLLLREPRYTLLVAACLCLAEVGITFWV
  IHRVAYTEIDWKAYMAEVEGVINGTYDYTQLQGDTGPLVYPAGFVYIFMGLYYATSRGTD
  IRMAQNIFAVLYLATLLLVFLIYHQTCKVPPFVFFFMCCASYRVHSIFVLRLFNDPVAMV
  LLFLSINLLLAQRWGWGCCFFSLAVSVKMNVLLFAPGLLFLLLTQFGFRGALPKLGICAG
  LQVVLGLPFLLENPSGYLSRSFDLGRQFLFHWTVNWRFLPEALFLHRAFHLALLTAHLTL
  LLLFALCRWHRTGESILSLLRDPSKRKVPPQPLTPNQIVSTLFTSNFIGICFSRSLHYQF
  YVWYFHTLPYLLWAMPARWLTHLLRLLVLGLIELSWNTYPSTSCSSAALHICHAVILLQL
  WLGPQPFPKSTQHSKKAH

• Sequence length: 438

Pathways

KEGG:

N-Glycan biosynthesis
Various types of N-glycan biosynthesis
Metabolic pathways

Reactome:

Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
Defective ALG3 causes ALG3-CDG (CDG-1d)

Associated diseases

Causal
Disease term	Disease name	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
Congenital disorder of glycosylation	CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Id, ALG3-CDG	rs121434387, rs1264383808, rs766244312, rs1555497568, rs1555496968, rs267606740, rs1568296260, rs1562937199, rs28939378, rs121908583, rs1568757730, rs28936415, rs587776874, rs387906831, rs151173406, rs387907202, rs387907203, rs397515327, rs398124348, rs374928784, rs398124401, rs587777114, rs587777115, rs587777116, rs752922461, rs794727073, rs797044712, rs765191836, rs376663459, rs778210210, rs864309659, rs869025583, rs751325113, rs369160589, rs1085307116, rs1085307117, rs746019074, rs1135401817, rs773281248, rs1555575860, rs753780084, rs1553121545, rs764831063, rs1185483085, rs867045420, rs1554464495, rs1460811017, rs1297536872, rs1555388034, rs1334593208, rs1555493029, rs1555497604, rs1031719032, rs768656482, rs937887233, rs1272097668, rs1569508922, rs1048764460, rs373260156, rs1569547876, rs1563018529, rs777937112, rs1231928102, rs1584977236, rs1582461023, rs1422285851, rs139624629, rs1597225261, rs763516132, rs200605408, rs1596252105, rs1596252196, rs121908340, rs1596256204, rs553396382, rs1180515976, rs1299775990, rs1596261161, rs1596261208, rs1428414601, rs1596261268, rs16835020, rs1270276368, rs373355236, rs1582477100, rs747606976, rs2049726544, rs781115721, rs1926621737, rs1444255127, rs1663960324, rs1665467473, rs1431963909, rs1663959543, rs376870425	10581255, 16006436, 27604308, 19862844, 15840742
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
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
Optic atrophy	Optic Atrophy	rs121434508, rs267607017, rs80356524, rs80356525, rs879255560, rs104893753, rs80356529, rs397515360, rs104893620, rs199476104, rs199476112, rs199476118, rs398124298, rs770066665, rs398124299, rs61750185, rs672601379, rs727504060, rs786204830, rs794727804, rs199946797, rs863224127, rs863224131, rs863224134, rs863224906, rs372054380, rs886037828, rs764791523, rs145639028, rs1057519312, rs1064794257, rs1064794656, rs1064797303, rs774265764, rs760337383, rs1553784985, rs72653786, rs1555229948, rs1555119216, rs761743852, rs1553785338, rs1020764190, rs782581701, rs1560408865, rs761460379, rs773022324, rs782740998, rs1560327427, rs80356528, rs1734162973, rs1716524583, rs1057368575

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma of Lung	Associate	36575396, 39287231
Carcinoma Non Small Cell Lung	Associate	31899049
Congenital Disorders of Glycosylation	Associate	26805780, 32389449, 32655146, 34440401, 35211808
Death	Associate	32655146
Epilepsy	Associate	32389449
Hemangioma	Associate	32389449
Inflammation	Associate	37308935
Lymphatic Metastasis	Stimulate	31899049
Muscular Dystrophy Congenital Type 1D	Associate	32389449
Nasopharyngeal Carcinoma	Associate	40083705
Neoplasm Metastasis	Stimulate	40312703
Neoplasms	Associate	31899049, 40312703
Urinary Bladder Neoplasms	Associate	40312703
Uterine Cervical Neoplasms	Associate	17504382