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    TMEM59 transmembrane protein 59 [ Homo sapiens (human) ]

    Gene ID: 9528, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TMEM59provided by HGNC
    Official Full Name
    transmembrane protein 59provided by HGNC
    Primary source
    HGNC:HGNC:1239
    See related
    Ensembl:ENSG00000116209 MIM:617084; AllianceGenome:HGNC:1239
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DCF1; C1orf8; PRO195; UNQ169; HSPC001
    Summary
    This gene encodes a protein shown to regulate autophagy in response to bacterial infection. This protein may also regulate the retention of amyloid precursor protein (APP) in the Golgi apparatus through its control of APP glycosylation. Overexpression of this protein has been found to promote apoptosis in a glioma cell line. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
    Expression
    Ubiquitous expression in colon (RPKM 47.8), prostate (RPKM 39.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM59 in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (54026681..54053573, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53909583..53936476, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54492354..54519246, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 12 Neighboring gene low density lipoprotein receptor class A domain containing 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:54485757-54486258 Neighboring gene MPRA-validated peak239 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 915 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:54518370-54518924 and GRCh37_chr1:54518925-54519480 Neighboring gene transcription elongation factor A N-terminal and central domain containing 2 Neighboring gene microRNA 4781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1053 Neighboring gene COX7B pseudogene 3

    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. Dendritic cell factor 1 inhibits proliferation and migration and induces apoptosis of neuroblastoma cells by inhibiting the ERK signaling pathway. Luo G, et al. Oncol Rep, 2019 Jan. PMID 30365123, Free PMC Article
    2. TMEM59 potentiates Wnt signaling by promoting signalosome formation. Gerlach JP, et al. Proc Natl Acad Sci U S A, 2018 Apr 24. PMID 29632210, Free PMC Article
    3. DCF1 subcellular localization and its function in mitochondria. Chen Y, et al. Biochimie, 2018 Jan. PMID 29074393
    4. Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex. Bakulski KM, et al. J Alzheimers Dis, 2012. PMID 22451312, Free PMC Article
    5. Dcf1 induces glioblastoma cells apoptosis by blocking autophagy. Luo G, et al. Cancer Med, 2022 Jan. PMID 34799992, Free PMC Article

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircTMEM59 Serves as miR-410-3p Sponge to Inhibit the Proliferation and Metastasis of Colorectal Cancer by Regulating HOXD8.
      Title: CircTMEM59 Serves as miR-410-3p Sponge to Inhibit the Proliferation and Metastasis of Colorectal Cancer by Regulating HOXD8.
    2. Dcf1 induces glioblastoma cells apoptosis by blocking autophagy.
      Title: Dcf1 induces glioblastoma cells apoptosis by blocking autophagy.
    3. Dcf1 alleviates C99-mediated deficits in drosophila by reducing the cleavage of C99.
      Title: Dcf1 alleviates C99-mediated deficits in drosophila by reducing the cleavage of C99.
    4. The Chlamydia effector CT622/TaiP targets a nonautophagy related function of ATG16L1.
      Title: The Chlamydia effector CT622/TaiP targets a nonautophagy related function of ATG16L1.
    5. Results provide evidence that DCF1 plays an important role in controlling neuroblastoma (NB) tumor viability, promoting cell apoptosis, and inhibiting tumorigenesis in vivo. DCF1 could be a potential new inhibitor for components of the ERK1/2 signaling pathway and helped understand the molecular mechanism of NB.
      Title: Dendritic cell factor 1 inhibits proliferation and migration and induces apoptosis of neuroblastoma cells by inhibiting the ERK signaling pathway.
    6. identify the single-span membrane protein TMEM59 as an interactor of FZD and LRP6 and a positive regulator of Wnt signaling. Mechanistically, TMEM59 promotes the formation of multimeric Wnt-FZD assemblies via intramembrane interactions.
      Title: TMEM59 potentiates Wnt signaling by promoting signalosome formation.
    7. DCF1 subcellular localization and its function in mitochondria
      Title: DCF1 subcellular localization and its function in mitochondria.
    8. The TMEM59 gene identified from our discovery approach was recently implicated in amyloid-beta protein precursor post-translational processing, supporting a role for epigenetic change in LOAD pathology.
      Title: Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex.
    9. TMEM59 affects amyloid precursor protein shedding by reducing its acccess to cellular components.
      Title: The novel membrane protein TMEM59 modulates complex glycosylation, cell surface expression, and secretion of the amyloid precursor protein.
    10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    Clone Names

    • FLJ14422, FLJ26177, FLJ33090, FLJ42977, FLJ90155

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of protein localization to plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within_negative_effect protein glycosylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi cis cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi medial cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi trans cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    is_active_in late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane protein 59
    Names
    dendritic cell factor 1
    liver membrane-bound protein

    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_001305043.2 → NP_001291972.1  transmembrane protein 59 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001291972.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF290615, AK057652, AL353898, BC016374, CA776407
      UniProtKB/TrEMBL
      Q5T704
      Conserved Domains (1) summary
      pfam12280
      Location:72 → 257
      BSMAP; Brain specific membrane anchored protein

    2. NM_001305049.1 → NP_001291978.1  transmembrane protein 59 isoform 3

      See identical proteins and their annotated locations for NP_001291978.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) includes an alternate 5' terminal exon resulting in a distinct 5' UTR and translation initiation at an in-frame downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AF290615, AK057652, AL353898, BP371330, BX463615, CA776407, DB459209
      UniProtKB/TrEMBL
      Q6P5R1
      Conserved Domains (1) summary
      pfam12280
      Location:1 → 126
      BSMAP; Brain specific membrane anchored protein

    3. NM_001305050.2 → NP_001291979.1  transmembrane protein 59 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001291979.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons in the 5' coding region compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AF290615, AK057652, AL353898, BI604139, CA776407
      UniProtKB/TrEMBL
      Q6P5R1
      Conserved Domains (1) summary
      pfam12280
      Location:48 → 190
      BSMAP; Brain specific membrane anchored protein

    4. NM_001305051.1 → NP_001291980.1  transmembrane protein 59 isoform 6

      See identical proteins and their annotated locations for NP_001291980.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) includes an alternate 5' terminal exon, uses an alternate splice site in its 5' coding region and initiates translation at an in-frame downstream start codon. The encoded isoform (6) is shorter than isoform 1. Variants 6 and 7 encode the same isoform (6).
      Source sequence(s)
      AF290615, AK057652, AL353898, BP371330, BU165003, CA776407, DB459209
      Consensus CDS
      CCDS81329.1
      UniProtKB/TrEMBL
      A0A9K3Y7R5, D3DQ49, Q5T6Z8, Q6P5R1
      Related
      ENSP00000360392.1, ENST00000371341.5
      Conserved Domains (1) summary
      pfam12280
      Location:1 → 125
      BSMAP; Brain specific membrane anchored protein

    5. NM_001305052.1 → NP_001291981.1  transmembrane protein 59 isoform 6

      See identical proteins and their annotated locations for NP_001291981.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) includes two alternate exons in its 5' UTR, uses an alternate splice site in its 5' coding region and initiates translation at an in-frame downstream start codon. The encoded isoform (6) is shorter than isoform 1. Variants 6 and 7 encode the same isoform (6).
      Source sequence(s)
      AF290615, AK057652, AL353898, BF574560, BP371330, CA776407, DB459209
      Consensus CDS
      CCDS81329.1
      UniProtKB/TrEMBL
      A0A9K3Y7R5, D3DQ49, Q5T6Z8, Q6P5R1
      Related
      ENSP00000360395.1, ENST00000371344.5
      Conserved Domains (1) summary
      pfam12280
      Location:1 → 125
      BSMAP; Brain specific membrane anchored protein

    6. NM_001305066.2 → NP_001291995.1  transmembrane protein 59 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several exons compared to variant 1 and its 3' terminal exon extends past a splice site that is used in variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AF290615, AL353898, BM979433
      Consensus CDS
      CCDS81330.1
      UniProtKB/TrEMBL
      Q5T703
      Related
      ENSP00000360388.3, ENST00000371337.3
      Conserved Domains (1) summary
      pfam12280
      Location:72 → 130
      BSMAP; Brain specific membrane anchored protein

    7. NM_004872.5 → NP_004863.2  transmembrane protein 59 isoform 2 precursor

      See identical proteins and their annotated locations for NP_004863.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is one amino acid shorter and includes a single amino acid substitution compared to isoform 1.
      Source sequence(s)
      AF290615, AK057652, AL353898, CA776407
      Consensus CDS
      CCDS586.1
      UniProtKB/Swiss-Prot
      B3KQL7, O75393, Q4VBP9, Q5T705, Q96KX7, Q9BXS4
      UniProtKB/TrEMBL
      Q5T704
      Related
      ENSP00000234831.5, ENST00000234831.10
      Conserved Domains (1) summary
      pfam12280
      Location:72 → 256
      BSMAP; Brain specific membrane anchored protein

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      54026681..54053573 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      53909583..53936476 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BXS4.1 GenPept UniProtKB/Swiss-Prot:Q9BXS4

    Gene LinkOut

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

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