SMG9 (SMG9 nonsense mediated mRNA decay factor)

Gene

• Entrez ID: 56006
• Gene name: SMG9 nonsense mediated mRNA decay factor
• Gene symbol: SMG9
• Synonyms: C19orf61, F17127_1, HBMS, NEDITPO
• Chromosome: 19
• Chromosome location: 19q13.31
• Summary: This gene encodes a regulatory subunit of the SMG1 complex, which plays a critical role in nonsense-mediated mRNA decay (NMD). Binding of the encoded protein to the SMG1 complex kinase scaffold protein results in the inhibition of its kinase activity. Mut

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs869312741	GG>-	Likely-pathogenic, pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs869312742	T>C	Likely-pathogenic, pathogenic	Intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2111238	hsa-miR-1276	CLIP-seq
MIRT2111239	hsa-miR-3158-3p	CLIP-seq
MIRT2111240	hsa-miR-3202	CLIP-seq
MIRT2111241	hsa-miR-323b-3p	CLIP-seq
MIRT2111242	hsa-miR-4311	CLIP-seq
MIRT2111243	hsa-miR-4747-5p	CLIP-seq
MIRT2111244	hsa-miR-5095	CLIP-seq
MIRT2111245	hsa-miR-583	CLIP-seq
MIRT2111246	hsa-miR-600	CLIP-seq
MIRT2111239	hsa-miR-3158-3p	CLIP-seq
MIRT2111240	hsa-miR-3202	CLIP-seq
MIRT2111243	hsa-miR-4747-5p	CLIP-seq
MIRT2111244	hsa-miR-5095	CLIP-seq
MIRT2111246	hsa-miR-600	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA	21873635
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP	19417104
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	TAS
GO:0001654	Process	Eye development	ISS
GO:0001701	Process	In utero embryonic development	IEA
GO:0005515	Function	Protein binding	IPI	19417104, 20817927, 25416956, 26496610, 32296183
GO:0005829	Component	Cytosol	TAS
GO:0007420	Process	Brain development	ISS
GO:0007507	Process	Heart development	ISS
GO:0042802	Function	Identical protein binding	IPI	20817927

Other IDs

• MIM: 613176
• HGNC: 25763
• e!Ensembl: ENSG00000105771

Protein

• UniProt ID: Q9H0W8
• Protein name: Nonsense-mediated mRNA decay factor SMG9
• Protein function: Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons (PubMed:19417104). Is recruited by release factors to stalled ribosomes together with SMG1 and SMG8 (forming the SMG1C protein kinase complex) and, in the SMG1C
• PDB: 6L54, 6SYT, 6Z3R, 7PW4, 7PW5, 7PW7, 7PW8, 7PW9, 8FE7
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF10220	Smg8_Smg9	198 → 351	Smg8_Smg9	Family

• Sequence:

  MSESGHSQPGLYGIERRRRWKEPGSGGPQNLSGPGGRERDYIAPWERERRDASEETSTSV
  MQKTPIILSKPPAERSKQPPPPTAPAAPPAPAPLEKPIVLMKPREEGKGPVAVTGASTPE
  GTAPPPPAAPAPPKGEKEGQRPTQPVYQIQNRGMGTAAPAAMDPVVGQAKLLPPERMKHS
  IKLVDDQMNWCDSAIEYLLDQTDVLVVGVLGLQGTGKSMVMSLLSANTPEEDQRTYVFRA
  QSAEMKERGGNQTSGIDFFITQERIVFLDTQPILSPSILDHLINNDRKLPPEYNLPHTYV
  EMQSLQIAAFLFTVCHVVIVVQDWFTDLSLYRFLQTAEMVKPSTPSPSHESSSSSGSDEG
  TEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQLMAHSHLRYKGTLSMLQCNVFPGLPPD
  FLDSEVNLFLVPFMDSEAESENPPRAGPGSSPLFSLLPGYRGHPSFQSLVSKLRSQVMSM
  ARPQLSHTILTEKNWFHYAARIWDGVRKSSALAEYSRLLA

• Sequence length: 520

Pathways

Reactome:

Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
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	27018474
Heart and brain malformation syndrome	HEART AND BRAIN MALFORMATION SYNDROME	rs869312741	31390136, 27018474
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
Microphthalmos	Microphthalmos	rs794726862, rs1329285216
Ventricular septal defect	Ventricular Septal Defects	rs104894073, rs387906775

Unknown
Disease name	Disease term	dbSNP ID	References
Cerebral atrophy	Cerebral atrophy
Dandy-walker syndrome	Dandy-Walker Syndrome
Gastroesophageal reflux disease	Gastroesophageal reflux disease
Hypoplasia of corpus callosum	Hypoplasia of corpus callosum
Interrupted aortic arch	Interrupted aortic arch
Posteriorly rotated ear	Posteriorly rotated ear