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    TM6SF2 transmembrane 6 superfamily member 2 [ Homo sapiens (human) ]

    Gene ID: 53345, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TM6SF2provided by HGNC
    Official Full Name
    transmembrane 6 superfamily member 2provided by HGNC
    Primary source
    HGNC:HGNC:11861
    See related
    Ensembl:ENSG00000213996 MIM:606563; AllianceGenome:HGNC:11861
    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
    Enables identical protein binding activity. Involved in regulation of lipid metabolic process. Located in endoplasmic reticulum membrane and endoplasmic reticulum-Golgi intermediate compartment membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in duodenum (RPKM 49.9), small intestine (RPKM 45.9) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See TM6SF2 in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19264366..19273301, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19401816..19410753, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19375175..19384110, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene neurocan Neighboring gene RNA, U6 small nuclear 1028, pseudogene Neighboring gene hyaluronan and proteoglycan link protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19380555-19381056 Neighboring gene SURP and G-patch domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19431454-19432425 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:19446492-19447691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19447717-19448218 Neighboring gene MAU2 sister chromatid cohesion factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19452846-19453354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19459741-19460241 Neighboring gene uncharacterized LOC124904656

    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. TM6SF2 E167K variant predicts severe liver fibrosis for human immunodeficiency/hepatitis C virus co-infected patients, and severe steatosis only for a non-3 hepatitis C virus genotype. Sagnelli C, et al. World J Gastroenterol, 2016 Oct 14. PMID 27784963, Free PMC Article
    2. Role of TM6SF2 rs58542926 in the pathogenesis of nonalcoholic pediatric fatty liver disease: A multiethnic study. Goffredo M, et al. Hepatology, 2016 Jan. PMID 26457389, Free PMC Article
    3. Transmembrane-6 superfamily member 2 (TM6SF2) E167K variant increases susceptibility to hepatic steatosis in obese children. Mancina RM, et al. Dig Liver Dis, 2016 Jan. PMID 26520056
    4. Associations of TM6SF2 167K allele with liver enzymes and lipid profile in children: the PANIC Study. Viitasalo A, et al. Pediatr Res, 2016 May. PMID 26756786
    5. Diverse impacts of the rs58542926 E167K variant in TM6SF2 on viral and metabolic liver disease phenotypes. Eslam M, et al. Hepatology, 2016 Jul. PMID 26822232

    See all (105) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. G-quadruplex forming regions in GCK and TM6SF2 are targets for differential DNA methylation in metabolic disease and hepatocellular carcinoma patients.
      Title: G-quadruplex forming regions in GCK and TM6SF2 are targets for differential DNA methylation in metabolic disease and hepatocellular carcinoma patients.
    2. The common p.Ile291Val variant of ERLIN1 enhances TM6SF2 function and is associated with protection against MASLD.
      Title: The common p.Ile291Val variant of ERLIN1 enhances TM6SF2 function and is associated with protection against MASLD.
    3. No association of NAFLD-related polymorphisms in PNPLA3 and TM6SF2 with all-cause and cardiovascular mortality in an Austrian population study.
      Title: No association of NAFLD-related polymorphisms in PNPLA3 and TM6SF2 with all-cause and cardiovascular mortality in an Austrian population study.
    4. Basic and translational evidence supporting the role of TM6SF2 in VLDL metabolism.
      Title: Basic and translational evidence supporting the role of TM6SF2 in VLDL metabolism.
    5. A study of genetic variants, genetic risk score and DNA methylation of PNPLA3 and TM6SF2 in alcohol liver cirrhosis.
      Title: A study of genetic variants, genetic risk score and DNA methylation of PNPLA3 and TM6SF2 in alcohol liver cirrhosis.
    6. Effects of TM6SF2 rs58542926 polymorphism on hepatocellular lipids and insulin resistance in early type 2 diabetes.
      Title: Effects of TM6SF2 rs58542926 polymorphism on hepatocellular lipids and insulin resistance in early type 2 diabetes.
    7. The impact of transmembrane 6 superfamily 2 (TM6SF2) rs58542926 on liver-related events in patients with advanced chronic liver disease.
      Title: The impact of transmembrane 6 superfamily 2 (TM6SF2) rs58542926 on liver-related events in patients with advanced chronic liver disease.
    8. Metabolic disorders induced by PNPLA3 and TM6SF2 gene variants affect chronic kidney disease in patients infected with non-genotype 3 hepatitis C virus.
      Title: Metabolic disorders induced by PNPLA3 and TM6SF2 gene variants affect chronic kidney disease in patients infected with non-genotype 3 hepatitis C virus.
    9. Association of PNPLA3 (rs738409) & TM6SF2 (rs58542926) and ATG16L1 (rs2241880) genetic variants with susceptibility to hepatocellular carcinoma in a group of Egyptian patients with HCV-induced liver cirrhosis.
      Title: Association of PNPLA3 (rs738409) & TM6SF2 (rs58542926) and ATG16L1 (rs2241880) genetic variants with susceptibility to hepatocellular carcinoma in a group of Egyptian patients with HCV-induced liver cirrhosis.
    10. TM6SF2-rs58542926 Genetic Variant Modifies the Protective Effect of a "Prudent" Dietary Pattern on Serum Triglyceride Levels.
      Title: TM6SF2-rs58542926 Genetic Variant Modifies the Protective Effect of a "Prudent" Dietary Pattern on Serum Triglyceride Levels.
    Submit: New GeneRIF Correction See all GeneRIFs (97)

    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
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: HAPLN4

    Homology

    Clone Names

    • KIAA1926

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lipid homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of lipid metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of lipid metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum-Golgi intermediate compartment membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transmembrane 6 superfamily member 2

    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_001001524.3 → NP_001001524.2  transmembrane 6 superfamily member 2

      See identical proteins and their annotated locations for NP_001001524.2

      Status: VALIDATED

      Source sequence(s)
      AC003967, AF255923, AK097070, DA930032
      Consensus CDS
      CCDS42528.1
      UniProtKB/Swiss-Prot
      Q0IJ64, Q9BZW4
      Related
      ENSP00000374014.2, ENST00000389363.5
      Conserved Domains (1) summary
      cd21106
      Location:7 → 361
      TM6SF1-like; transmembrane 6 superfamily member 1, member 2, and similar proteins

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      19264366..19273301 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      19401816..19410753 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_203510.1: Suppressed sequence

      Description
      NM_203510.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZW4.3 GenPept UniProtKB/Swiss-Prot:Q9BZW4

    Gene LinkOut

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

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