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

Gene ID: 123920, updated on 9-Jun-2025
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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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

Go to nucleotide: Graphics FASTA GenBank

  • 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

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)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

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
acts_upstream_of_or_within blastocyst hatching IEA
Inferred from Electronic Annotation
more info
  
involved_in chemotaxis IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within 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 cytoplasm IEA
Inferred from Electronic Annotation
more info
  
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 membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear membrane IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
CKLF-like MARVEL transmembrane domain-containing protein 3
Names
chemokine-like factor superfamily member 3

NEW Try the new Transcript table

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

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