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

Gene ID: 51460, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52903572..53046073, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52936457..53078977, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. 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
  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_2023_10

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

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