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TMEM59 transmembrane protein 59 [ Homo sapiens (human) ]

Gene ID: 9528, updated on 28-Oct-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
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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

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