SMG9 (SMG9 nonsense mediated mRNA decay factor)

Gene

• Entrez ID: 56006
• Gene name: SMG9 nonsense mediated mRNA decay factor
• Gene symbol: SMG9
• Synonyms (NCBI Gene): 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
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA
GO:0000184	Process	Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP	19417104
GO:0001654	Process	Eye development	IEA
GO:0001654	Process	Eye development	ISS
GO:0001701	Process	In utero embryonic development	IEA
GO:0005515	Function	Protein binding	IPI	19417104, 20817927, 25220460, 25416956, 26496610, 26841701, 32296183, 33205750
GO:0005829	Component	Cytosol	TAS
GO:0007420	Process	Brain development	IEA
GO:0007420	Process	Brain development	ISS
GO:0007507	Process	Heart development	IEA
GO:0007507	Process	Heart development	ISS
GO:0042802	Function	Identical protein binding	IPI	20817927
GO:0043066	Process	Negative regulation of apoptotic process	EXP	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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Abnormal cardiovascular system morphology	Likely pathogenic	rs869312741	RCV000210059
Abnormal facial shape	Likely pathogenic	rs869312741	RCV000210059
Brainstem dysplasia	Likely pathogenic	rs869312741	RCV000210059
Global developmental delay	Likely pathogenic	rs869312741	RCV000210059
Heart and brain malformation syndrome	Likely pathogenic; Pathogenic	rs869312741, rs1418644001, rs1968559161	RCV000210947 RCV003756641 RCV003152621
Neurodevelopmental abnormality	Pathogenic	rs1968559161	RCV001264652
Neurodevelopmental disorder with intention tremor, pyramidal signs, dyspraxia, and ocular anomalies	Pathogenic	rs749498958, rs377252810	RCV002274864 RCV004587784

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Autism spectrum disorder	association	rs372754806	RCV001291442
SMG9-related disorder	Likely benign; Benign	rs1174892147, rs2513899357, rs138335943, rs184145466, rs148972113, rs28483837, rs150580575, rs902928896	RCV003902200 RCV003943998 RCV003952165 RCV003944547 RCV003961576 RCV003914549 RCV003914752 RCV003957353

Associations from Text Mining
Disease Name	Relationship Type	References
Apraxias	Associate	35087184
beta Thalassemia	Associate	2434529
Brain Diseases	Associate	35321723
Developmental Disabilities	Associate	33242396, 35087184
Facial Dysmorphism with Multiple Malformations	Associate	33242396
Failure to Thrive	Associate	35321723
Genetic Diseases Inborn	Associate	35321723
Growth Disorders	Associate	35321723
Heart Defects Congenital	Associate	33242396
Immunologic Deficiency Syndromes	Inhibit	35321723
Immunologic Deficiency Syndromes	Associate	35321723
Intellectual Disability	Associate	35087184, 35321723
Microcephaly	Associate	33242396, 35321723
Splenomegaly	Associate	2434529
Tremor	Associate	35087184