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    SFMBT1 Scm like with four mbt domains 1 [ Homo sapiens (human) ]

    Gene ID: 51460, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SFMBT1provided by HGNC
    Official Full Name
    Scm like with four mbt domains 1provided by HGNC
    Primary source
    HGNC:HGNC:20255
    See related
    Ensembl:ENSG00000163935 MIM:607319; AllianceGenome:HGNC:20255
    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
    RU1; SFMBT; hSFMBT
    Summary
    This gene shares high similarity with the Drosophila Scm (sex comb on midleg) gene. It encodes a protein which contains four malignant brain tumor repeat (mbt) domains and may be involved in antigen recognition. [provided by RefSeq, Jun 2012]
    Expression
    Broad expression in testis (RPKM 14.1), kidney (RPKM 2.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SFMBT1 in Genome Data Viewer
    Location:
    3p21.1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52903572..53046073, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52936457..53078977, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52937588..53080089, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene STIMATE-MUSTN1 readthrough Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52873819-52874320 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52878501-52879001 Neighboring gene STIM activating enhancer Neighboring gene musculoskeletal, embryonic nuclear protein 1 Neighboring gene microRNA 8064 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:52906559-52906829 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14454 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70661 Neighboring gene Sharpr-MPRA regulatory region 7399 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:53032540-53033040 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:53033923-53034166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19949 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:53064883-53065417 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53080405-53080906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53080907-53081406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53106949-53107566 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 3047 Neighboring gene RFT1 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19952 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53136831-53137332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19953 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53148350-53149549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19954

    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 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. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells. Morel S, et al. Immunity, 2000 Jan. PMID 10661410
    2. Segmental copy number loss of SFMBT1 gene in elderly individuals with ventriculomegaly: a community-based study. Kato T, et al. Intern Med, 2011. PMID 21325761
    3. A Segmental Copy Number Loss of the SFMBT1 Gene Is a Genetic Risk for Shunt-Responsive, Idiopathic Normal Pressure Hydrocephalus (iNPH): A Case-Control Study. Sato H, et al. PLoS One, 2016. PMID 27861535, Free PMC Article
    4. Genome-wide copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population. Chung RH, et al. BMC Genomics, 2017 Aug 8. PMID 28789618, Free PMC Article
    5. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Yuan Y, et al. Hum Mol Genet, 2021 Apr 27. PMID 33481017, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Regulatory Variant rs2535629 in ITIH3 Intron Confers Schizophrenia Risk By Regulating CTCF Binding and SFMBT1 Expression.
      Title: Regulatory Variant rs2535629 in ITIH3 Intron Confers Schizophrenia Risk By Regulating CTCF Binding and SFMBT1 Expression.
    2. Multi-omics analysis to identify susceptibility genes for colorectal cancer.
      Title: Multi-omics analysis to identify susceptibility genes for colorectal cancer.
    3. High SFMBT1 expression is associated with clear cell renal cell carcinomas.
      Title: Genome-wide Screening Identifies SFMBT1 as an Oncogenic Driver in Cancer with VHL Loss.
    4. SFMBT1 knockdown was demonstrated to inhibit cell growth and induced apoptosis, which was consistent with the function of miR-20a- 3p upregulation in HaCaT cells.
      Title: MiR-20a-3p regulates TGF-β1/Survivin pathway to affect keratinocytes proliferation and apoptosis by targeting SFMBT1 in vitro.
    5. copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population
      Title: Genome-wide copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population.
    6. The present study demonstrates that a copy number loss within intron 2 of the SFMBT1 gene may be a genetic risk factor for shunt-responsive definite iNPH.
      Title: A Segmental Copy Number Loss of the SFMBT1 Gene Is a Genetic Risk for Shunt-Responsive, Idiopathic Normal Pressure Hydrocephalus (iNPH): A Case-Control Study.
    7. The malignant brain tumor (MBT) domain protein SFMBT1 is an integral histone reader subunit of the LSD1 demethylase complex for chromatin association and epithelial-to-mesenchymal transition.
      Title: The malignant brain tumor (MBT) domain protein SFMBT1 is an integral histone reader subunit of the LSD1 demethylase complex for chromatin association and epithelial-to-mesenchymal transition.
    8. When bound to its gene targets, SFMBT1 recruits its associated proteins and causes chromatin compaction and transcriptional repression
      Title: SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors.
    9. novel mechanisms accounting for SFMBT1-mediated transcription repression and revealed an essential role of Sfmbt1 in regulating MyoD-mediated transcriptional silencing
      Title: Proteomic and functional analyses reveal the role of chromatin reader SFMBT1 in regulating epigenetic silencing and the myogenic gene program.
    10. Data identified IGF1, SLC4A4, WWOX, and SFMBT1 as hypertension susceptibility genes by gene based association scan and gene expression analysis.
      Title: Identification of IGF1, SLC4A4, WWOX, and SFMBT1 as hypertension susceptibility genes in Han Chinese with a genome-wide gene-based association study.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat downregulates the expression of Scm-like with four mbt domains 1 (SFMBT1) in human primary T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp434L243

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of muscle organ development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    scm-like with four MBT domains protein 1
    Names
    Scm-related gene containing four mbt domains
    Scm-related gene product containing four mbt domains
    renal ubiquitous protein 1

    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.

    mRNA and Protein(s)

    1. NM_016329.4 → NP_057413.2  scm-like with four MBT domains protein 1

      See identical proteins and their annotated locations for NP_057413.2

      Status: REVIEWED

      Source sequence(s)
      AC096887, AC099667, AI206996, BC014614, DB085221
      Consensus CDS
      CCDS2867.1
      UniProtKB/Swiss-Prot
      Q402F7, Q96C73, Q9UHJ3, Q9Y4Q9
      Related
      ENSP00000378235.2, ENST00000394752.8
      Conserved Domains (4) summary
      cd09581
      Location:782 → 866
      SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
      smart00454
      Location:793 → 857
      SAM; Sterile alpha motif
      smart00561
      Location:23 → 120
      MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
      pfam12140
      Location:502 → 617
      DUF3588; Protein of unknown function (DUF3588)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      52903572..53046073 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      52936457..53078977 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001005158.2: Suppressed sequence

      Description
      NM_001005158.2: This RefSeq was permanently suppressed because currently there is no full-length support for the transcript.

    2. NM_001005159.2: Suppressed sequence

      Description
      NM_001005159.2: This RefSeq was permanently suppressed because currently there is no full-length support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UHJ3.2 GenPept UniProtKB/Swiss-Prot:Q9UHJ3

    Gene LinkOut

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

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