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Aliases for CMTM6 Gene

Aliases for CMTM6 Gene

  • CKLF Like MARVEL Transmembrane Domain Containing 6 2 3 5
  • Chemokine-Like Factor Superfamily Member 6 3 4
  • Chemokine-Like Factor Super Family 6 2 3
  • Chemokine-Like Factor Superfamily 6 2 3
  • CKLFSF6 3 4
  • CKLF-Like MARVEL Transmembrane Domain-Containing Protein 6 3
  • CKLF-Like MARVEL Transmembrane Domain Containing 6 2
  • PRO2219 3

External Ids for CMTM6 Gene

Previous HGNC Symbols for CMTM6 Gene

  • CKLFSF6

Summaries for CMTM6 Gene

Entrez Gene Summary for CMTM6 Gene

  • This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and transmembrane 4 superfamilies. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 3. This gene is widely expressed in many tissues, but the exact function of the encoded protein is unknown. [provided by RefSeq, Jul 2008]

GeneCards Summary for CMTM6 Gene

CMTM6 (CKLF Like MARVEL Transmembrane Domain Containing 6) is a Protein Coding gene. Among its related pathways are Innate Immune System. Gene Ontology (GO) annotations related to this gene include cytokine activity. An important paralog of this gene is CMTM4.

UniProtKB/Swiss-Prot for CMTM6 Gene

  • Master regulator of recycling and plasma membrane expression of PD-L1/CD274, an immune inhibitory ligand critical for immune tolerance to self and antitumor immunity. Associates with both constitutive and IFNG-induced PD-L1/CD274 at recycling endosomes, where it protects PD-L1/CD274 from being targeted for lysosomal degradation, likely by preventing its STUB1-mediated ubiquitination. May stabilize PD-L1/CD274 expression on antigen presenting cells and potentiates inhibitory signaling by PDCD1/CD279, its receptor on T-cells, ultimately triggering T-cell anergy.

Additional gene information for CMTM6 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CMTM6 Gene

Genomics for CMTM6 Gene

GeneHancer (GH) Regulatory Elements for CMTM6 Gene

Promoters and enhancers for CMTM6 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
GH03J032501 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 666.7 +1.1 1068 2.7 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 CMTM6 CNOT10 UBP1 DYNC1LI1 SUGT1P2 CNOT10-AS1 GC03P032466
GH03J032468 Enhancer 1.3 Ensembl ENCODE dbSUPER 18 +33.3 33330 2.3 HDGF FOXA2 NEUROD1 FEZF1 ZNF2 IRF4 ZNF207 ATF7 FOS RUNX3 CMTM6 RPL31P18 CMTM7 GC03P032466
GH03J033437 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 9.8 -936.5 -936529 5.5 CLOCK ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC UBP1 PIR40256 CNOT10 PDCD6IP FBXL2 GLB1 TMPPE CMTM6 GC03M033417
GH03J031530 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 9.8 +970.5 970540 5.1 CLOCK MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 SP3 GC03M031530 STT3B ZNF860 CMTM6 GC03P031521 GC03M031604
GH03J032430 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 15.5 +71.0 70951 3.3 PKNOX1 CEBPG FEZF1 ZFHX2 ATF7 IKZF2 RUNX3 CREM SRF ZNF687 CMTM6 RPL31P18 DYNC1LI1 CMTM7 GC03M031988 GC03P032466
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CMTM6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CMTM6 gene promoter:
  • FOXL1
  • CP2
  • C/EBPalpha
  • RelA
  • NF-kappaB1
  • NF-kappaB
  • SRF (504 AA)
  • SRF
  • RORalpha1

Genomic Locations for CMTM6 Gene

Genomic Locations for CMTM6 Gene
chr3:32,481,312-32,503,408
(GRCh38/hg38)
Size:
22,097 bases
Orientation:
Minus strand
chr3:32,522,804-32,544,900
(GRCh37/hg19)
Size:
22,097 bases
Orientation:
Minus strand

Genomic View for CMTM6 Gene

Genes around CMTM6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CMTM6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CMTM6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CMTM6 Gene

Proteins for CMTM6 Gene

  • Protein details for CMTM6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NX76-CKLF6_HUMAN
    Recommended name:
    CKLF-like MARVEL transmembrane domain-containing protein 6
    Protein Accession:
    Q9NX76
    Secondary Accessions:
    • Q6IAC4

    Protein attributes for CMTM6 Gene

    Size:
    183 amino acids
    Molecular mass:
    20419 Da
    Quaternary structure:
    • Interacts with PD-L1/CD274 (via transmembrane domain); the interaction is direct (PubMed:28813417, PubMed:28813410). Interacts with CMTM4 (PubMed:28813410). Interacts with CD58, ARG1, ENO1 and TMPO (PubMed:28813417).

neXtProt entry for CMTM6 Gene

Post-translational modifications for CMTM6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CMTM6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CMTM6 Gene

Domains & Families for CMTM6 Gene

Gene Families for CMTM6 Gene

Protein Domains for CMTM6 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for CMTM6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NX76

UniProtKB/Swiss-Prot:

CKLF6_HUMAN :
  • Belongs to the chemokine-like factor family.
Family:
  • Belongs to the chemokine-like factor family.
genes like me logo Genes that share domains with CMTM6: view

Function for CMTM6 Gene

Molecular function for CMTM6 Gene

UniProtKB/Swiss-Prot Function:
Master regulator of recycling and plasma membrane expression of PD-L1/CD274, an immune inhibitory ligand critical for immune tolerance to self and antitumor immunity. Associates with both constitutive and IFNG-induced PD-L1/CD274 at recycling endosomes, where it protects PD-L1/CD274 from being targeted for lysosomal degradation, likely by preventing its STUB1-mediated ubiquitination. May stabilize PD-L1/CD274 expression on antigen presenting cells and potentiates inhibitory signaling by PDCD1/CD279, its receptor on T-cells, ultimately triggering T-cell anergy.

Phenotypes From GWAS Catalog for CMTM6 Gene

Gene Ontology (GO) - Molecular Function for CMTM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA --
GO:0005515 protein binding IPI 28813410
genes like me logo Genes that share ontologies with CMTM6: view
genes like me logo Genes that share phenotypes with CMTM6: view

Animal Model Products

miRNA for CMTM6 Gene

miRTarBase miRNAs that target CMTM6

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CMTM6 Gene

Localization for CMTM6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CMTM6 Gene

Cell membrane; Multi-pass membrane protein. Early endosome membrane; Multi-pass membrane protein. Recycling endosome membrane; Multi-pass membrane protein. Note=Co-localizes with PD-L1/CD274 in the plasma membrane and in recycling endosomes. {ECO:0000269 PubMed:28813417}.

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 CMTM6 gene
Compartment Confidence
plasma membrane 5
extracellular 5
lysosome 4
cytoskeleton 2
cytosol 2
endosome 1

Gene Ontology (GO) - Cellular Components for CMTM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane HDA 19946888
GO:0016021 integral component of membrane IBA --
GO:0035577 azurophil granule membrane TAS --
genes like me logo Genes that share ontologies with CMTM6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CMTM6 Gene

Pathways & Interactions for CMTM6 Gene

genes like me logo Genes that share pathways with CMTM6: view

Pathways by source for CMTM6 Gene

3 Reactome pathways for CMTM6 Gene

Gene Ontology (GO) - Biological Process for CMTM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006935 chemotaxis IEA --
GO:0010469 regulation of signaling receptor activity IEA --
GO:0043312 neutrophil degranulation TAS --
genes like me logo Genes that share ontologies with CMTM6: view

No data available for SIGNOR curated interactions for CMTM6 Gene

Drugs & Compounds for CMTM6 Gene

No Compound Related Data Available

Transcripts for CMTM6 Gene

mRNA/cDNA for CMTM6 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(542) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CMTM6 Gene

CKLF-like MARVEL transmembrane domain containing 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CMTM6 Gene

No ASD Table

Relevant External Links for CMTM6 Gene

GeneLoc Exon Structure for
CMTM6
ECgene alternative splicing isoforms for
CMTM6

Expression for CMTM6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CMTM6 Gene

mRNA differential expression in normal tissues according to GTEx for CMTM6 Gene

This gene is overexpressed in Whole Blood (x5.9).

Protein differential expression in normal tissues from HIPED for CMTM6 Gene

This gene is overexpressed in Monocytes (26.7), Bone (9.2), and Peripheral blood mononuclear cells (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CMTM6 Gene



NURSA nuclear receptor signaling pathways regulating expression of CMTM6 Gene:

CMTM6

SOURCE GeneReport for Unigene cluster for CMTM6 Gene:

Hs.380627

mRNA Expression by UniProt/SwissProt for CMTM6 Gene:

Q9NX76-CKLF6_HUMAN
Tissue specificity: Expressed in the leukocytes, placenta and testis.

Evidence on tissue expression from TISSUES for CMTM6 Gene

  • Blood(4.4)
  • Lung(2)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with CMTM6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CMTM6 Gene

Orthologs for CMTM6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CMTM6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CMTM6 34 33
  • 99.64 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CMTM6 34 33
  • 81.14 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cmtm6 33
  • 79.42 (n)
mouse
(Mus musculus)
Mammalia Cmtm6 16 34 33
  • 77.96 (n)
cow
(Bos Taurus)
Mammalia CMTM6 34 33
  • 75.46 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CMTM6 34
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CMTM6 34
  • 54 (a)
OneToOne
chicken
(Gallus gallus)
Aves CMTM6 34 33
  • 56.93 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CMTM6 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cmtm6 33
  • 49.52 (n)
zebrafish
(Danio rerio)
Actinopterygii cmtm6 34 33
  • 46.29 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2454 34
  • 13 (a)
OneToMany
Species where no ortholog for CMTM6 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)
  • 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 CMTM6 Gene

ENSEMBL:
Gene Tree for CMTM6 (if available)
TreeFam:
Gene Tree for CMTM6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CMTM6: view image

Paralogs for CMTM6 Gene

Paralogs for CMTM6 Gene

(1) SIMAP similar genes for CMTM6 Gene using alignment to 1 proteins:

  • CKLF6_HUMAN

Pseudogenes.org Pseudogenes for CMTM6 Gene

genes like me logo Genes that share paralogs with CMTM6: view

Variants for CMTM6 Gene

Sequence variations from dbSNP and Humsavar for CMTM6 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000017925 -- 32,484,287(-) T/A intron_variant
rs1000047242 -- 32,501,115(-) G/A intron_variant
rs1000234027 -- 32,481,160(-) A/G downstream_transcript_variant
rs1000239822 -- 32,481,721(-) C/T 3_prime_UTR_variant
rs1000286400 -- 32,481,409(-) A/C 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for CMTM6 Gene

Variant ID Type Subtype PubMed ID
esv3595776 CNV loss 21293372
nsv1003285 CNV gain 25217958
nsv834652 CNV loss 17160897

Variation tolerance for CMTM6 Gene

Residual Variation Intolerance Score: 60.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.54; 29.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CMTM6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CMTM6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CMTM6 Gene

Disorders for CMTM6 Gene

Additional Disease Information for CMTM6

No disorders were found for CMTM6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CMTM6 Gene

Publications for CMTM6 Gene

  1. Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. (PMID: 28813410) Mezzadra R … Schumacher TNM (Nature 2017) 3 4 58
  2. CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity. (PMID: 28813417) Burr ML … Dawson MA (Nature 2017) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Identification of eight genes encoding chemokine-like factor superfamily members 1-8 (CKLFSF1-8) by in silico cloning and experimental validation. (PMID: 12782130) Han W … Ma D (Genomics 2003) 3 4 58

Products for CMTM6 Gene

Sources for CMTM6 Gene

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