Aliases for TM6SF2 Gene

Aliases for TM6SF2 Gene

  • Transmembrane 6 Superfamily Member 2 2 3 4 5

External Ids for TM6SF2 Gene

Previous GeneCards Identifiers for TM6SF2 Gene

  • GC19M019859
  • GC19M019756
  • GC19M019210
  • GC19M019226
  • GC19M019228
  • GC19M019236
  • GC19M019375
  • GC19M018938

Summaries for TM6SF2 Gene

GeneCards Summary for TM6SF2 Gene

TM6SF2 (Transmembrane 6 Superfamily Member 2) is a Protein Coding gene. Diseases associated with TM6SF2 include Fatty Liver Disease and Lipid Storage Disease. An important paralog of this gene is TM6SF1.

UniProtKB/Swiss-Prot Summary for TM6SF2 Gene

  • Regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content (PubMed:24531328, PubMed:24927523). May function as sterol isomerase (PubMed:25566323).

Additional gene information for TM6SF2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TM6SF2 Gene

Genomics for TM6SF2 Gene

GeneHancer (GH) Regulatory Elements for TM6SF2 Gene

Promoters and enhancers for TM6SF2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J019271 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas 750.6 +0.5 489 2.2 SP5 RXRA ZSCAN4 SP1 SAP130 ZBTB25 HNF4A SIN3A ARID4B ETV4 ENSG00000267629 TM6SF2 lnc-TM6SF2-1 NDUFA13 GATAD2A MAU2 piR-50437-343
GH19J019274 Enhancer 0.5 ENCODE 750.6 -1.7 -1706 1.4 SP1 RXRA MNT JUND HNF4A RAD21 HNF4G ZNF398 ENSG00000267629 TM6SF2 lnc-TM6SF2-1 NDUFA13 GATAD2A lnc-TM6SF2-2
GH19J019402 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.4 -132.0 -132043 5.3 ZNF785 ZBTB40 SP1 CTCF MLX RBPJ SMARCE1 POLR2A NR2F1 MIXL1 lnc-MAU2-1 GATAD2A NDUFA13 NR2C2AP ZNF101 TMEM161A ENSG00000268030 TM6SF2 ZNF90 ZNF682
GH19J019641 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 4.9 -369.7 -369681 3.1 CTCF ZBTB6 POLR2A MYC CC2D1A ELF1 RAD21 ZNF121 MNT ZNF148 GMIP LPAR2 TM6SF2 lnc-LPAR2-1 lnc-ZNF101-1
GH19J019456 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4 -187.9 -187874 9.5 ETV6 DACH1 NFIB ZNF652 SP1 MAFK BACH1 MLLT1 SP7 ZNF687 GATAD2A NDUFA13 GMIP MIR640 MAU2 TM6SF2 RFXANK PBX4 ZNF14 ZNF506
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TM6SF2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TM6SF2 gene promoter:
  • AML1a
  • COMP1
  • E47
  • FOXC1
  • GATA-1
  • GATA-2
  • GATA-3
  • Lmo2
  • NF-1
  • NF-1/L

Genomic Locations for TM6SF2 Gene

Genomic Locations for TM6SF2 Gene
chr19:19,264,364-19,273,391
(GRCh38/hg38)
Size:
9,028 bases
Orientation:
Minus strand
chr19:19,375,173-19,384,200
(GRCh37/hg19)
Size:
9,028 bases
Orientation:
Minus strand

Genomic View for TM6SF2 Gene

Genes around TM6SF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TM6SF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TM6SF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TM6SF2 Gene

Proteins for TM6SF2 Gene

  • Protein details for TM6SF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BZW4-TM6S2_HUMAN
    Recommended name:
    Transmembrane 6 superfamily member 2
    Protein Accession:
    Q9BZW4
    Secondary Accessions:
    • Q0IJ64

    Protein attributes for TM6SF2 Gene

    Size:
    377 amino acids
    Molecular mass:
    42554 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for TM6SF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TM6SF2 Gene

Post-translational modifications for TM6SF2 Gene

No Post-translational modifications

Other Protein References for TM6SF2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TM6SF2 Gene

Domains & Families for TM6SF2 Gene

Gene Families for TM6SF2 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for TM6SF2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TM6SF2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ39751 fis, clone SMINT2017855 (Q8N8A7_HUMAN)
  • Transmembrane 6 superfamily member 2 (TM6S2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BZW4

UniProtKB/Swiss-Prot:

TM6S2_HUMAN :
  • Belongs to the TM6SF family.
Family:
  • Belongs to the TM6SF family.
genes like me logo Genes that share domains with TM6SF2: view

Function for TM6SF2 Gene

Molecular function for TM6SF2 Gene

UniProtKB/Swiss-Prot Function:
Regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content (PubMed:24531328, PubMed:24927523). May function as sterol isomerase (PubMed:25566323).

Phenotypes From GWAS Catalog for TM6SF2 Gene

Gene Ontology (GO) - Molecular Function for TM6SF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with TM6SF2: view
genes like me logo Genes that share phenotypes with TM6SF2: view

Animal Models for TM6SF2 Gene

MGI Knock Outs for TM6SF2:
  • Tm6sf2 Tm6sf2<tm1a(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TM6SF2 Gene

Localization for TM6SF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TM6SF2 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein. Endoplasmic reticulum-Golgi intermediate compartment membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TM6SF2 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 3
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for TM6SF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IBA,IDA 24927523
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane IBA,IDA 24927523
genes like me logo Genes that share ontologies with TM6SF2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TM6SF2 Gene

Pathways & Interactions for TM6SF2 Gene

PathCards logo

SuperPathways for TM6SF2 Gene

No Data Available

Interacting Proteins for TM6SF2 Gene

Gene Ontology (GO) - Biological Process for TM6SF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0019216 regulation of lipid metabolic process IDA,IBA 24927523
GO:0055088 lipid homeostasis IBA 21873635
genes like me logo Genes that share ontologies with TM6SF2: view

No data available for Pathways by source and SIGNOR curated interactions for TM6SF2 Gene

Drugs & Compounds for TM6SF2 Gene

No Compound Related Data Available

Transcripts for TM6SF2 Gene

mRNA/cDNA for TM6SF2 Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TM6SF2 Gene

No ASD Table

Relevant External Links for TM6SF2 Gene

GeneLoc Exon Structure for
TM6SF2
ECgene alternative splicing isoforms for
TM6SF2

Expression for TM6SF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TM6SF2 Gene

mRNA differential expression in normal tissues according to GTEx for TM6SF2 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x21.0) and Liver (x16.0).

NURSA nuclear receptor signaling pathways regulating expression of TM6SF2 Gene:

TM6SF2

SOURCE GeneReport for Unigene cluster for TM6SF2 Gene:

Hs.531624

mRNA Expression by UniProt/SwissProt for TM6SF2 Gene:

Q9BZW4-TM6S2_HUMAN
Tissue specificity: Substantial expression in liver and intestine, whereas all other tissues analyzed show low levels.

Evidence on tissue expression from TISSUES for TM6SF2 Gene

  • Liver(3.1)
genes like me logo Genes that share expression patterns with TM6SF2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for TM6SF2 Gene

Orthologs for TM6SF2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TM6SF2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TM6SF2 33 32
  • 99.65 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TM6SF2 33 32
  • 85.2 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TM6SF2 33 32
  • 84.66 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Tm6sf2 17 33 32
  • 80.71 (n)
rat
(Rattus norvegicus)
Mammalia Tm6sf2 32
  • 80.55 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TM6SF2 33
  • 67 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TM6SF2 33
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves TM6SF2 33 32
  • 65.83 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tm6sf2 32
  • 59.89 (n)
zebrafish
(Danio rerio)
Actinopterygii tm6sf2 33 32
  • 54.42 (n)
OneToMany
TM6SF2 (2 of 2) 33
  • 45 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5317 33
  • 28 (a)
ManyToMany
-- 33
  • 22 (a)
ManyToMany
Species where no ortholog for TM6SF2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TM6SF2 Gene

ENSEMBL:
Gene Tree for TM6SF2 (if available)
TreeFam:
Gene Tree for TM6SF2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TM6SF2: view image

Paralogs for TM6SF2 Gene

Paralogs for TM6SF2 Gene

(1) SIMAP similar genes for TM6SF2 Gene using alignment to 1 proteins:

  • TM6S2_HUMAN
genes like me logo Genes that share paralogs with TM6SF2: view

Variants for TM6SF2 Gene

Sequence variations from dbSNP and Humsavar for TM6SF2 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000474557 -- 19,272,694(-) T/G intron_variant
rs1000600182 -- 19,266,886(-) A/G intron_variant
rs1001071362 -- 19,271,051(-) C/T coding_sequence_variant, missense_variant
rs1001528360 -- 19,272,303(-) G/A intron_variant
rs1001608650 -- 19,264,219(-) G/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for TM6SF2 Gene

Variant ID Type Subtype PubMed ID
nsv1151217 CNV deletion 26484159

Variation tolerance for TM6SF2 Gene

Residual Variation Intolerance Score: 78.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.62; 65.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TM6SF2 Gene

Human Gene Mutation Database (HGMD)
TM6SF2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TM6SF2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TM6SF2 Gene

Disorders for TM6SF2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for TM6SF2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
fatty liver disease
  • steatosis of liver
lipid storage disease
  • inborn lipid storage disorder
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TM6SF2

genes like me logo Genes that share disorders with TM6SF2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TM6SF2 Gene

Publications for TM6SF2 Gene

  1. Cloning of the novel gene TM6SF1 reveals conservation of clusters of paralogous genes between human chromosomes 15q24-->q26 and 19p13.3-->p12. (PMID: 11124529) Carim-Todd L … Sumoy L (Cytogenetics and cell genetics 2000) 2 3 4 56
  2. TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease. (PMID: 24978903) Liu YL … Anstee QM (Nature communications 2014) 3 4 56
  3. TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content. (PMID: 24927523) Mahdessian H … van't Hooft F (Proceedings of the National Academy of Sciences of the United States of America 2014) 3 4 56
  4. Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease. (PMID: 24531328) Kozlitina J … Cohen JC (Nature genetics 2014) 3 4 56
  5. Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk. (PMID: 24633158) Holmen OL … Willer CJ (Nature genetics 2014) 3 4 56

Products for TM6SF2 Gene

Sources for TM6SF2 Gene