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    CMTM3 CKLF like MARVEL transmembrane domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 123920, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CMTM3provided by HGNC
    Official Full Name
    CKLF like MARVEL transmembrane domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:19174
    See related
    Ensembl:ENSG00000140931 MIM:607886; AllianceGenome:HGNC:19174
    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
    BNAS2; CKLFSF3
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 24.7), placenta (RPKM 16.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CMTM3 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66603996..66613892)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72397883..72408187)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66637899..66647795)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene CKLF-CMTM1 readthrough Neighboring gene CKLF like MARVEL transmembrane domain containing 1 Neighboring gene CKLF like MARVEL transmembrane domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7561 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66642903-66643714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66653785-66654286 Neighboring gene CKLF like MARVEL transmembrane domain containing 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:66677635-66677813 Neighboring gene Sharpr-MPRA regulatory region 8452 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:66708833-66709036 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:66710611-66711112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66725551-66726230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66726231-66726910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66726911-66727590 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:66729849-66730688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7566 Neighboring gene dynein cytoplasmic 1 light intermediate chain 2 Neighboring gene MPRA-validated peak2616 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:66785153-66785868 Neighboring gene DYNC1LI2 divergent transcript Neighboring gene telomere repeat binding bouquet formation protein 1

    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. Familial hypereosinophilia associated with eosinophilic gastrointestinal symptoms in individuals with a missense mutation in CKLF-like MARVEL transmembrane domain containing 3. Wardlaw AJ, et al. Clin Exp Allergy, 2021 Nov. PMID 34048099
    2. 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. Wang Y, et al. Cancer Res, 2009 Jun 15. PMID 19509237
    3. Characterization and expression profile of CMTM3/CKLFSF3. Zhong J, et al. J Biochem Mol Biol, 2006 Sep 30. PMID 17002874
    4. CMTM3 is frequently reduced in clear cell renal cell carcinoma and exhibits tumor suppressor activities. Xie J, et al. Clin Transl Oncol, 2014 Apr. PMID 23907292
    5. CMTM3 inhibits cell migration and invasion and correlates with favorable prognosis in gastric cancer. Su Y, et al. Cancer Sci, 2014 Jan. PMID 24131472, Free PMC Article

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Familial hypereosinophilia associated with eosinophilic gastrointestinal symptoms in individuals with a missense mutation in CKLF-like MARVEL transmembrane domain containing 3.
      Title: Familial hypereosinophilia associated with eosinophilic gastrointestinal symptoms in individuals with a missense mutation in CKLF-like MARVEL transmembrane domain containing 3.
    2. CMTM3 exhibited a lower expression pattern in gastric cancer tissues.MiR-135b-5p promotes gastric cancer progression by targeting CMTM3.
      Title: miR-135b-5p promotes gastric cancer progression by targeting CMTM3.
    3. this study demonstrates that knockdown of CMTM3 promotes the metastasis of gastric cancer through the STAT3/Twist1/EMT pathway
      Title: Knockdown of CMTM3 promotes metastasis of gastric cancer via the STAT3/Twist1/EMT signaling pathway.
    4. CMTM3 was significantly hypermethylated in colorectal cancer tissues when compared with adjacent normal colorectal tissues.
      Title: DNA methylation of CMTM3, SSTR2, and MDFI genes in colorectal cancer.
    5. CMTM3 decreases EGFR expression, facilitates EGFR degradation, and inhibits the EGF-mediated tumorigenicity of gastric cancer cells by enhancing Rab5 activity.
      Title: CMTM3 decreases EGFR expression and EGF-mediated tumorigenicity by promoting Rab5 activity in gastric cancer.
    6. CMTM3 mediates cell-cell adhesion at adherens junctions and contributes to the control of vascular sprouting by regulation VE-cadherin turnover.
      Title: CMTM3 (CKLF-Like Marvel Transmembrane Domain 3) Mediates Angiogenesis by Regulating Cell Surface Availability of VE-Cadherin in Endothelial Adherens Junctions.
    7. Overexpression of CMTM3 attenuated the tumor growth of hepatocellular carcinoma.
      Title: CKLF-Like MARVEL Transmembrane Domain-Containing Member 3 (CMTM3) Inhibits the Proliferation and Tumorigenisis in Hepatocellular Carcinoma Cells.
    8. identified CMTM3 as a novel secretory protein released via exosomes in the prostate
      Title: CMTM3 presents a secreted form released via exosomes.
    9. study indicates that elevated CMTM3 methylation is a risk factor in male LSCC patients, especially in the patients with age over 55years and with smoking behavior
      Title: Elevated methylation of CMTM3 promoter in the male laryngeal squamous cell carcinoma patients.
    10. Reduced expression of CMTM3 is associated with prostate cancer.
      Title: CMTM3 is reduced in prostate cancer and inhibits migration, invasion and growth of LNCaP cells.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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

    • FLJ31762, MGC51956

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cytokine 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 blastocyst hatching IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chemotaxis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of B cell receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    CKLF-like MARVEL transmembrane domain-containing protein 3
    Names
    chemokine-like factor superfamily member 3

    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_001363918.2 → NP_001350847.1  CKLF-like MARVEL transmembrane domain-containing protein 3

      Status: REVIEWED

      Source sequence(s)
      AC018557
      Consensus CDS
      CCDS10815.1
      UniProtKB/Swiss-Prot
      A6NCL9, Q8IUU8, Q8IWQ6, Q8IYE2, Q8IZ39, Q8IZ59, Q96MX0
      Conserved Domains (1) summary
      pfam01284
      Location:36 → 149
      MARVEL; Membrane-associating domain

    2. NM_001363923.2 → NP_001350852.1  CKLF-like MARVEL transmembrane domain-containing protein 3

      Status: REVIEWED

      Source sequence(s)
      AC018557, AF479813, AK056324
      Consensus CDS
      CCDS10815.1
      UniProtKB/Swiss-Prot
      A6NCL9, Q8IUU8, Q8IWQ6, Q8IYE2, Q8IZ39, Q8IZ59, Q96MX0
      Related
      ENSP00000400482.2, ENST00000424011.6
      Conserved Domains (1) summary
      pfam01284
      Location:36 → 149
      MARVEL; Membrane-associating domain

    3. NM_144601.5 → NP_653202.1  CKLF-like MARVEL transmembrane domain-containing protein 3

      See identical proteins and their annotated locations for NP_653202.1

      Status: REVIEWED

      Source sequence(s)
      AC018557, AF479813
      Consensus CDS
      CCDS10815.1
      UniProtKB/Swiss-Prot
      A6NCL9, Q8IUU8, Q8IWQ6, Q8IYE2, Q8IZ39, Q8IZ59, Q96MX0
      Related
      ENSP00000354579.4, ENST00000361909.8
      Conserved Domains (1) summary
      pfam01284
      Location:36 → 149
      MARVEL; Membrane-associating domain

    4. NM_181553.4 → NP_853531.1  CKLF-like MARVEL transmembrane domain-containing protein 3

      See identical proteins and their annotated locations for NP_853531.1

      Status: REVIEWED

      Source sequence(s)
      AF479813, BC047701
      Consensus CDS
      CCDS10815.1
      UniProtKB/Swiss-Prot
      A6NCL9, Q8IUU8, Q8IWQ6, Q8IYE2, Q8IZ39, Q8IZ59, Q96MX0
      Related
      ENSP00000455851.1, ENST00000567572.6
      Conserved Domains (1) summary
      pfam01284
      Location:36 → 149
      MARVEL; Membrane-associating domain

    RNA

    1. NR_037619.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018557, AF479813, CT001840

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      66603996..66613892
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433594.1 → XP_047289550.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A6NCL9, Q8IUU8, Q8IWQ6, Q8IYE2, Q8IZ39, Q8IZ59, Q96MX0
      Related
      ENSP00000455758.1, ENST00000562707.5

    2. XM_047433597.1 → XP_047289553.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X3

      UniProtKB/TrEMBL
      H3BUD5
      Related
      ENSP00000457589.1, ENST00000564060.5

    3. XM_047433595.1 → XP_047289551.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X2

      UniProtKB/TrEMBL
      J3KSR6
      Related
      ENSP00000462613.1, ENST00000566756.5

    4. XM_047433598.1 → XP_047289554.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      72397883..72408187
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379558.1 → XP_054235533.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X5

    2. XM_054379557.1 → XP_054235532.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      A6NCL9, Q8IUU8, Q8IWQ6, Q8IYE2, Q8IZ39, Q8IZ59, Q96MX0

    3. XM_054379559.1 → XP_054235534.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X3

      UniProtKB/TrEMBL
      H3BUD5

    4. XM_054379560.1 → XP_054235535.1  CKLF-like MARVEL transmembrane domain-containing protein 3 isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001048251.1: Suppressed sequence

      Description
      NM_001048251.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.

    2. NM_181554.1: Suppressed sequence

      Description
      NM_181554.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    3. NM_181555.1: Suppressed sequence

      Description
      NM_181555.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript variant.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MX0.1 GenPept UniProtKB/Swiss-Prot:Q96MX0

    Gene LinkOut

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

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