U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 53345, updated on 5-Mar-2024

    Summary

    Go to the top of the page Help
    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, Apr 2022]
    Expression
    Biased expression in duodenum (RPKM 49.9), small intestine (RPKM 45.9) and 1 other tissue See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See TM6SF2 in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19264366..19273301, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19401816..19410753, complement)
    105.20220307 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. TM6SF2-rs58542926 Genetic Variant Modifies the Protective Effect of a "Prudent" Dietary Pattern on Serum Triglyceride Levels. Kalafati IP, et al. Nutrients, 2023 Feb 23. PMID 36904112, Free PMC Article
    2. Research progress on the relationship between TM6SF2 rs58542926 polymorphism and non-alcoholic fatty liver disease. Xue WY, et al. Expert Rev Gastroenterol Hepatol, 2022 Feb. PMID 35057689
    3. Perturbation of TM6SF2 Expression Alters Lipid Metabolism in a Human Liver Cell Line. Pant A, et al. Int J Mol Sci, 2021 Sep 9. PMID 34575933, Free PMC Article
    4. Effects of TM6SF2 E167K on hepatic lipid and very low-density lipoprotein metabolism in humans. Borén J, et al. JCI Insight, 2020 Dec 17. PMID 33170809, Free PMC Article
    5. Transmembrane 6 superfamily member 2 167K allele improves renal function in children with obesity. Marzuillo P, et al. Pediatr Res, 2020 Aug. PMID 31923913

    See all (98) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. Different effects of low muscle mass on the risk of non-alcoholic fatty liver disease and hepatic fibrosis in a prospective cohort.
      Title: Different effects of low muscle mass on the risk of non-alcoholic fatty liver disease and hepatic fibrosis in a prospective cohort.
    8. PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and cirrhosis in Pakistani chronic hepatitis C patients: a genetic association study.
      Title: PNPLA3 and TM6SF2 genetic variants and hepatic fibrosis and cirrhosis in Pakistani chronic hepatitis C patients: a genetic association study.
    9. TM6SF2/PNPLA3/MBOAT7 Loss-of-Function Genetic Variants Impact on NAFLD Development and Progression Both in Patients and in In Vitro Models.
      Title: TM6SF2/PNPLA3/MBOAT7 Loss-of-Function Genetic Variants Impact on NAFLD Development and Progression Both in Patients and in In Vitro Models.
    10. Effects of PNPLA3, TM6SF2 and SAMM50 on the development and severity of non-alcoholic fatty liver disease in children.
      Title: Effects of PNPLA3, TM6SF2 and SAMM50 on the development and severity of non-alcoholic fatty liver disease in children.
    Submit: New GeneRIF Correction See all GeneRIFs (93)

    Phenotypes

    Go to the top of the page Help

    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

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    transmembrane 6 superfamily member 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_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
      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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous