U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

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

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

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 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

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

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

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

Go to the top of the page Help
Preferred Names
transmembrane 6 superfamily member 1

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_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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous