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    TM6SF1 transmembrane 6 superfamily member 1 [ Homo sapiens (human) ]

    Gene ID: 53346, updated on 3-Apr-2024

    Summary

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    Official Symbol
    TM6SF1provided by HGNC
    Official Full Name
    transmembrane 6 superfamily member 1provided by HGNC
    Primary source
    HGNC:HGNC:11860
    See related
    Ensembl:ENSG00000136404 MIM:606562; AllianceGenome:HGNC:11860
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to be integral component of membrane. Predicted to be active in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in brain (RPKM 3.4), thyroid (RPKM 3.0) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TM6SF1 in Genome Data Viewer
    Location:
    15q25.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (83107645..83137408)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (80971671..81001423)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (83776397..83806160)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9970 Neighboring gene Sharpr-MPRA regulatory region 9115 Neighboring gene microRNA 4515 Neighboring gene uncharacterized LOC124903543 Neighboring gene uncharacterized LOC124903588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6761 Neighboring gene HDGF like 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:83826782-83827981 Neighboring gene NANOG hESC enhancer GRCh37_chr15:83835576-83836077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6762 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:83876873-83877486 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:83889876-83891075 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:83893658-83894857 Neighboring gene MPRA-validated peak2407 silencer Neighboring gene uncharacterized LOC105370932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:83952807-83953307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:83954077-83954577 Neighboring gene basonuclin zinc finger protein 1 Neighboring gene NANOG hESC enhancer GRCh37_chr15:83979362-83979907 Neighboring gene uncharacterized LOC105370933

    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. TM6SF2 reduces lipid accumulation in vascular smooth muscle cells by inhibiting LOX-1 and CD36 expression. Li TT, et al. Exp Cell Res, 2023 Aug 15. PMID 37271250
    2. Transmembrane 6 superfamily 1 (Tm6sf1) is a novel lysosomal transmembrane protein. Tam WY, et al. Protoplasma, 2015 Jul. PMID 25422095
    3. Validation of DNA promoter hypermethylation biomarkers in breast cancer--a short report. de Groot JS, et al. Cell Oncol (Dordr), 2014 Aug. PMID 25123395
    4. Cloning of the novel gene TM6SF1 reveals conservation of clusters of paralogous genes between human chromosomes 15q24-->q26 and 19p13.3-->p12. Carim-Todd L, et al. Cytogenet Cell Genet, 2000. PMID 11124529
    5. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Maruyama K, et al. Gene, 1994 Jan 28. PMID 8125298

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TM6SF2 reduces lipid accumulation in vascular smooth muscle cells by inhibiting LOX-1 and CD36 expression.
      Title: TM6SF2 reduces lipid accumulation in vascular smooth muscle cells by inhibiting LOX-1 and CD36 expression.
    2. Data conclude that AKR1B1 and TM6SF1 may serve as candidate methylation biomarkers for early breast cancer detection.
      Title: Validation of DNA promoter hypermethylation biomarkers in breast cancer--a short report.
    Submit: New GeneRIF Correction

    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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane 6 superfamily member 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_001144903.3 → NP_001138375.1  transmembrane 6 superfamily member 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC024270, AK292100, BC063487, DQ021909
      Consensus CDS
      CCDS45338.1
      UniProtKB/TrEMBL
      Q53FN6
      Related
      ENSP00000457477.1, ENST00000565774.5
      Conserved Domains (1) summary
      pfam10914
      Location:233 → 322
      DUF2781; Protein of unknown function (DUF2781)

    2. NM_001330385.3 → NP_001317314.1  transmembrane 6 superfamily member 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      Consensus CDS
      CCDS81915.1
      UniProtKB/TrEMBL
      Q6P4D7
      Related
      ENSP00000368700.6, ENST00000379390.10
      Conserved Domains (1) summary
      cl12494
      Location:6 → 160
      TM6SF1-like; transmembrane 6 superfamily member 1, member 2, and similar proteins

    3. NM_001353878.2 → NP_001340807.1  transmembrane 6 superfamily member 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      UniProtKB/TrEMBL
      Q53FN6
      Conserved Domains (1) summary
      pfam10914
      Location:217 → 307
      DUF2781; Protein of unknown function (DUF2781)

    4. NM_001353879.2 → NP_001340808.1  transmembrane 6 superfamily member 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      UniProtKB/TrEMBL
      B4DIF6
      Conserved Domains (1) summary
      pfam10914
      Location:126 → 262
      DUF2781; Protein of unknown function (DUF2781)

    5. NM_001353880.2 → NP_001340809.1  transmembrane 6 superfamily member 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      UniProtKB/TrEMBL
      B4DIF6
      Conserved Domains (1) summary
      pfam10914
      Location:142 → 231
      DUF2781; Protein of unknown function (DUF2781)

    6. NM_001353881.2 → NP_001340810.1  transmembrane 6 superfamily member 1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      Conserved Domains (1) summary
      pfam10914
      Location:69 → 205
      DUF2781; Protein of unknown function (DUF2781)

    7. NM_001353882.2 → NP_001340811.1  transmembrane 6 superfamily member 1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      Conserved Domains (1) summary
      pfam10914
      Location:69 → 205
      DUF2781; Protein of unknown function (DUF2781)

    8. NM_001353883.2 → NP_001340812.1  transmembrane 6 superfamily member 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      Conserved Domains (1) summary
      pfam10914
      Location:18 → 154
      DUF2781; Protein of unknown function (DUF2781)

    9. NM_001353884.2 → NP_001340813.1  transmembrane 6 superfamily member 1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      Conserved Domains (1) summary
      pfam10914
      Location:18 → 154
      DUF2781; Protein of unknown function (DUF2781)

    10. NM_023003.5 → NP_075379.2  transmembrane 6 superfamily member 1 isoform 1

      See identical proteins and their annotated locations for NP_075379.2

      Status: VALIDATED

      Source sequence(s)
      AC024270, AK292100, BC063487
      Consensus CDS
      CCDS10323.1
      UniProtKB/Swiss-Prot
      A8K7T5, H3BU56, Q4U0U5, Q9BZW5
      UniProtKB/TrEMBL
      Q53FN6
      Related
      ENSP00000317000.9, ENST00000322019.14
      Conserved Domains (1) summary
      pfam10914
      Location:217 → 353
      DUF2781; Protein of unknown function (DUF2781)

    RNA

    1. NR_148560.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      Related
      ENST00000379384.9

    2. NR_148561.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC024270, BC063487
      Related
      ENST00000258909.13

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      83107645..83137408
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521679.3 → XP_011519981.1  transmembrane 6 superfamily member 1 isoform X1

      UniProtKB/TrEMBL
      Q53FN6
      Conserved Domains (1) summary
      pfam10914
      Location:217 → 307
      DUF2781; Protein of unknown function (DUF2781)

    RNA

    1. XR_931848.3 RNA Sequence

    2. XR_007064460.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      80971671..81001423
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378215.1 → XP_054234190.1  transmembrane 6 superfamily member 1 isoform X1

    RNA

    1. XR_008488969.1 RNA Sequence

    2. XR_008488968.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZW5.2 GenPept UniProtKB/Swiss-Prot:Q9BZW5

    Gene LinkOut

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

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