TMEM59 transmembrane protein 59 [Homo sapiens (human)] - Gene

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Dcf1 induces glioblastoma cells apoptosis by blocking autophagy.
Title: Dcf1 induces glioblastoma cells apoptosis by blocking autophagy.
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.
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.
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.
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.
DCF1 subcellular localization and its function in mitochondria
Title: DCF1 subcellular localization and its function in mitochondria.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

SHGC-74842 (e-PCR)
- UniSTS:27154

SHGC-57881 (e-PCR)
- UniSTS:1048

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-74862 (e-PCR)
- UniSTS:15674

D1S1423 (e-PCR)
- UniSTS:149619

D17S1136 (e-PCR)
- UniSTS:473214

SGC33632 (e-PCR)
- UniSTS:67768

D11S2875 (e-PCR)
- UniSTS:152053

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 more info	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)

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
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
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
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
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
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
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