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    SMG9 SMG9 nonsense mediated mRNA decay factor [ Homo sapiens (human) ]

    Gene ID: 56006, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SMG9provided by HGNC
    Official Full Name
    SMG9 nonsense mediated mRNA decay factorprovided by HGNC
    Primary source
    HGNC:HGNC:25763
    See related
    Ensembl:ENSG00000105771 MIM:613176; AllianceGenome:HGNC:25763
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HBMS; NEDITPO; C19orf61; F17127_1
    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. Mutations in this gene cause a multiple congenital anomaly syndrome in human patients, characterized by brain malformation, congenital heart disease and other features. [provided by RefSeq, Jul 2016]
    Expression
    Broad expression in testis (RPKM 13.7), lymph node (RPKM 6.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19q13.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (43727983..43754962, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (46550715..46577698, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (44232135..44259114, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene phospholipase A2 inhibitor and Ly6/PLAUR domain-containing protein-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44204596-44205096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44220201-44220701 Neighboring gene immunity related GTPase cinema Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10729 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44268619-44268844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14739 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44270408-44270571 Neighboring gene CRISPRi-validated cis-regulatory element KCNN4 K1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44281957-44282457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10730 Neighboring gene potassium calcium-activated channel subfamily N member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44283513-44284012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10731 Neighboring gene CRISPRi-validated cis-regulatory element chr19.4589 Neighboring gene Sharpr-MPRA regulatory region 14970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44288851-44289352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44289353-44289852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14743 Neighboring gene LY6/PLAUR domain containing 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of a novel compound heterozygous SMG9 variants in a Chinese family with heart and brain malformation syndrome using whole exome sequencing. Yang Q, et al. BMC Med Genomics, 2022 Mar 23. PMID 35321723, Free PMC Article
    2. A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development. Rahikkala E, et al. Eur J Hum Genet, 2022 May. PMID 35087184, Free PMC Article
    3. SMG9-deficiency syndrome caused by a homozygous missense variant: Expanding the genotypic and phenotypic spectrum of this developmental disorder. Lemire G, et al. Am J Med Genet A, 2020 Jul. PMID 32412169
    4. Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait. Abdel-Salam GMH, et al. Am J Med Genet A, 2022 Feb. PMID 34761517
    5. SMG9 drives ferroptosis by directly inhibiting GPX4 degradation. Han L, et al. Biochem Biophys Res Commun, 2021 Aug 27. PMID 34146907

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of a novel compound heterozygous SMG9 variants in a Chinese family with heart and brain malformation syndrome using whole exome sequencing.
      Title: Identification of a novel compound heterozygous SMG9 variants in a Chinese family with heart and brain malformation syndrome using whole exome sequencing.
    2. A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development.
      Title: A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development.
    3. Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait.
      Title: Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait.
    4. SMG9 drives ferroptosis by directly inhibiting GPX4 degradation.
      Title: SMG9 drives ferroptosis by directly inhibiting GPX4 degradation.
    5. SMG9-deficiency syndrome caused by a homozygous missense variant: Expanding the genotypic and phenotypic spectrum of this developmental disorder.
      Title: SMG9-deficiency syndrome caused by a homozygous missense variant: Expanding the genotypic and phenotypic spectrum of this developmental disorder.
    6. Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity.
      Title: Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity.
    7. Cryo-EM structure of SMG1-SMG8-SMG9 complex.
      Title: Cryo-EM structure of SMG1-SMG8-SMG9 complex.
    8. This study reports the 3.45-A resolution cryo-EM structure of human SMG1-SMG8-SMG9, a phosphatidylinositol-3-kinase (PI(3)K)-related protein kinase (PIKK) complex central to messenger RNA surveillance.
      Title: InsP(6) binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.
    9. These results indicated that miR-4651 regulated Nonsense-mediated mRNA decay by targeting SMG9 mRNA.
      Title: MicroRNA 4651 regulates nonsense-mediated mRNA decay by targeting SMG9 mRNA.
    10. Mutations in SMG9 cause a multiple congenital anomaly syndrome in humans and mice
      Title: Mutations in SMG9, Encoding an Essential Component of Nonsense-Mediated Decay Machinery, Cause a Multiple Congenital Anomaly Syndrome in Humans and Mice.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Heart and brain malformation syndrome
    MedGen: C4310793 OMIM: 616920 GeneReviews: Not available
    		Compare labs
    Neurodevelopmental disorder with intention tremor, pyramidal signs, dyspraxia, and ocular anomalies
    MedGen: C5774196 OMIM: 619995 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12886, DKFZp564H1322

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in eye development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in heart development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of apoptotic process EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    nonsense-mediated mRNA decay factor SMG9
    Names
    protein smg-9 homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_051200.1 RefSeqGene

      Range
      5075..32054
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_019108.4 → NP_061981.2  nonsense-mediated mRNA decay factor SMG9

      See identical proteins and their annotated locations for NP_061981.2

      Status: REVIEWED

      Source sequence(s)
      AC004780, AL136606, BQ180848, HY084349
      Consensus CDS
      CCDS33043.2
      UniProtKB/Swiss-Prot
      O60429, Q9H0W8, Q9H9A9
      Related
      ENSP00000270066.6, ENST00000270066.11

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      43727983..43754962 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005259057.4 → XP_005259114.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

      See identical proteins and their annotated locations for XP_005259114.1

      Related
      ENSP00000471398.1, ENST00000601170.5

    2. XM_011527113.2 → XP_011525415.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

      See identical proteins and their annotated locations for XP_011525415.1

    3. XM_011527114.2 → XP_011525416.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

      See identical proteins and their annotated locations for XP_011525416.1

    4. XM_011527115.2 → XP_011525417.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

      See identical proteins and their annotated locations for XP_011525417.1

    5. XM_047439098.1 → XP_047295054.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

    6. XM_011527116.2 → XP_011525418.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

      See identical proteins and their annotated locations for XP_011525418.1

    7. XM_047439099.1 → XP_047295055.1  nonsense-mediated mRNA decay factor SMG9 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      46550715..46577698 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321458.1 → XP_054177433.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

    2. XM_054321459.1 → XP_054177434.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

    3. XM_054321460.1 → XP_054177435.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

    4. XM_054321461.1 → XP_054177436.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

    5. XM_054321462.1 → XP_054177437.1  nonsense-mediated mRNA decay factor SMG9 isoform X1

    6. XM_054321463.1 → XP_054177438.1  nonsense-mediated mRNA decay factor SMG9 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H0W8.1 GenPept UniProtKB/Swiss-Prot:Q9H0W8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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