Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CMTM3 Gene

Aliases for CMTM3 Gene

  • CKLF Like MARVEL Transmembrane Domain Containing 3 2 3 5
  • Chemokine-Like Factor Superfamily Member 3 3 4
  • CKLFSF3 3 4
  • CKLF-Like MARVEL Transmembrane Domain-Containing Protein 3 3
  • CKLF-Like MARVEL Transmembrane Domain Containing 3 2
  • Chemokine-Like Factor Superfamily 3 2
  • BNAS2 3

External Ids for CMTM3 Gene

Previous HGNC Symbols for CMTM3 Gene


Previous GeneCards Identifiers for CMTM3 Gene

  • GC16P065196
  • GC16P052514

Summaries for CMTM3 Gene

Entrez Gene Summary for CMTM3 Gene

  • This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and the transmembrane 4 superfamilies of signaling molecules. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 16. Alternatively spliced transcript variants containing different 5' UTRs, but encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for CMTM3 Gene

CMTM3 (CKLF Like MARVEL Transmembrane Domain Containing 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include cytokine activity. An important paralog of this gene is CMTM5.

Additional gene information for CMTM3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CMTM3 Gene

Genomics for CMTM3 Gene

GeneHancer (GH) Regulatory Elements for CMTM3 Gene

Promoters and enhancers for CMTM3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J066603 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 658.2 +1.0 1000 3.6 HDGF PKNOX1 FOXA2 ARNT MLX ARID4B SIN3A DMAP1 ZNF766 ZNF143 CMTM3 CTCF NAE1 TK2 BEAN1 ZDHHC1 ENSG00000260465 ENSG00000259804 FBXL8 CES2
GH16J066695 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 12.1 +92.5 92527 2.5 SIN3A ZNF2 ZNF48 POLR2B GLIS2 ZNF213 ZNF143 KLF7 SP3 MXD4 CMTM4 GC16P066696 ACD CTCF BEAN1 CMTM3 NAE1 CA7 ENSG00000259804 GC16M066696
GH16J066580 Enhancer 0.9 Ensembl ENCODE 22.4 -22.6 -22577 2.2 CTCF PKNOX1 INSM2 RAD21 HIC1 ZNF335 ZNF366 EGR1 SCRT2 ZSCAN5C CMTM2 ENSG00000260650 BEAN1 CMTM3 CKLF CKLF-CMTM1 TK2
GH16J066749 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 7.4 +147.3 147271 2.7 SMAD1 ARNT SIN3A DMAP1 YY1 POLR2B ZNF766 ZNF207 ZNF143 KLF13 DYNC1LI2 ENSG00000246777 NAE1 ACD CTCF CES2 ENSG00000259804 TERB1 CMTM3 ENSG00000260558
GH16J066650 Enhancer 1.1 Ensembl ENCODE 7 +47.2 47237 1.1 ARNT ARID4B FEZF1 ARID2 ZNF143 ATF7 RUNX3 KAT8 SSRP1 RFX3 BEAN1 CMTM4 ENSG00000246777 DYNC1LI2 TK2 CMTM3 GC16P066646 GC16M066667
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CMTM3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CMTM3 gene promoter:
  • NF-kappaB
  • NF-kappaB1

Genomic Locations for CMTM3 Gene

Genomic Locations for CMTM3 Gene
10,019 bases
Plus strand
10,019 bases
Plus strand

Genomic View for CMTM3 Gene

Genes around CMTM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CMTM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CMTM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CMTM3 Gene

Proteins for CMTM3 Gene

  • Protein details for CMTM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    CKLF-like MARVEL transmembrane domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • A6NCL9
    • Q8IUU8
    • Q8IWQ6
    • Q8IYE2
    • Q8IZ39
    • Q8IZ59

    Protein attributes for CMTM3 Gene

    182 amino acids
    Molecular mass:
    19714 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CMTM3 Gene


neXtProt entry for CMTM3 Gene

Post-translational modifications for CMTM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CMTM3 Gene

Domains & Families for CMTM3 Gene

Gene Families for CMTM3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CMTM3 Gene


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the chemokine-like factor family.
  • Belongs to the chemokine-like factor family.
genes like me logo Genes that share domains with CMTM3: view

Function for CMTM3 Gene

Phenotypes From GWAS Catalog for CMTM3 Gene

Gene Ontology (GO) - Molecular Function for CMTM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005125 cytokine activity IEA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with CMTM3: view
genes like me logo Genes that share phenotypes with CMTM3: view

Animal Model Products

miRNA for CMTM3 Gene

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CMTM3 Gene

Localization for CMTM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CMTM3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

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 CMTM3 gene
Compartment Confidence
plasma membrane 3
extracellular 3
nucleus 3
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CMTM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IEA --
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA,IEA --
GO:0031965 nuclear membrane IEA --
genes like me logo Genes that share ontologies with CMTM3: view

Pathways & Interactions for CMTM3 Gene

SuperPathways for CMTM3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CMTM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006935 chemotaxis IEA --
GO:0010469 regulation of signaling receptor activity IEA --
GO:0050861 positive regulation of B cell receptor signaling pathway IEA --
genes like me logo Genes that share ontologies with CMTM3: view

No data available for Pathways by source and SIGNOR curated interactions for CMTM3 Gene

Drugs & Compounds for CMTM3 Gene

No Compound Related Data Available

Transcripts for CMTM3 Gene

Unigene Clusters for CMTM3 Gene

CKLF-like MARVEL transmembrane domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CMTM3 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d · 8e · 8f ^ 9
SP1: - - - - - - -
SP2: - - -
SP3: - -
SP4: - - -
SP5: -
SP6: - - - - -
SP7: - - - -
SP8: - -
SP9: - - - - - - - - - - - - - -

Relevant External Links for CMTM3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CMTM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CMTM3 Gene

mRNA differential expression in normal tissues according to GTEx for CMTM3 Gene

This gene is overexpressed in Whole Blood (x5.3).

Protein differential expression in normal tissues from HIPED for CMTM3 Gene

This gene is overexpressed in Placenta (25.6), Fetal testis (14.8), Ovary (10.9), Testis (7.5), and NK cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CMTM3 Gene

Protein tissue co-expression partners for CMTM3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CMTM3 Gene:


SOURCE GeneReport for Unigene cluster for CMTM3 Gene:


mRNA Expression by UniProt/SwissProt for CMTM3 Gene:

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

Evidence on tissue expression from TISSUES for CMTM3 Gene

  • Nervous system(4.6)
  • Lung(4.3)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with CMTM3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for CMTM3 Gene

Orthologs for CMTM3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CMTM3 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia CMTM3 34 33
  • 90.17 (n)
(Pan troglodytes)
Mammalia CMTM3 34 33
  • 89.63 (n)
(Bos Taurus)
Mammalia CMTM3 34 33
  • 89.08 (n)
(Mus musculus)
Mammalia Cmtm3 16 34 33
  • 85.71 (n)
(Rattus norvegicus)
Mammalia Cmtm3 33
  • 83.7 (n)
(Monodelphis domestica)
Mammalia CMTM3 34
  • 61 (a)
(Gallus gallus)
Aves CMTM3 34 33
  • 69.17 (n)
(Anolis carolinensis)
Reptilia CMTM3 34
  • 52 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cmtm3 33
  • 63.77 (n)
Str.9768 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.9811 33
(Danio rerio)
Actinopterygii cmtm3 34 33
  • 65.8 (n)
Species where no ortholog for CMTM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 CMTM3 Gene

Gene Tree for CMTM3 (if available)
Gene Tree for CMTM3 (if available)
Evolutionary constrained regions (ECRs) for CMTM3: view image

Paralogs for CMTM3 Gene

Paralogs for CMTM3 Gene

(2) SIMAP similar genes for CMTM3 Gene using alignment to 8 proteins:

  • H3BN06_HUMAN
  • H3BU39_HUMAN
  • I3L3C2_HUMAN
genes like me logo Genes that share paralogs with CMTM3: view

Variants for CMTM3 Gene

Sequence variations from dbSNP and Humsavar for CMTM3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000200038 -- 66,605,063(+) C/A intron_variant
rs1000626248 -- 66,611,219(+) G/A intron_variant
rs1000739094 -- 66,606,618(+) T/C intron_variant
rs1000830569 -- 66,613,833(+) G/A 3_prime_UTR_variant, non_coding_transcript_variant
rs1000982628 -- 66,606,349(+) G/C intron_variant

Variation tolerance for CMTM3 Gene

Residual Variation Intolerance Score: 43.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.40; 8.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CMTM3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CMTM3 Gene

Disorders for CMTM3 Gene

Additional Disease Information for CMTM3

No disorders were found for CMTM3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CMTM3 Gene

Publications for CMTM3 Gene

  1. CMTM3, located at the critical tumor suppressor locus 16q22.1, is silenced by CpG methylation in carcinomas and inhibits tumor cell growth through inducing apoptosis. (PMID: 19509237) Wang Y … Han W (Cancer research 2009) 3 22 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. 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
  4. Identification and characterization of a novel BASH N terminus-associated protein, BNAS2. (PMID: 15087455) Imamura Y … Kitamura D (The Journal of biological chemistry 2004) 2 3 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 CMTM3 Gene

Sources for CMTM3 Gene

Loading form....