CMTM3

gene
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Also known as FLJ31762BNAS2

Summary

CMTM3 (CKLF like MARVEL transmembrane domain containing 3, HGNC:19174) is a protein-coding gene on chromosome 16q22.1, encoding CKLF-like MARVEL transmembrane domain-containing protein 3 (Q96MX0).

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.

Source: NCBI Gene 123920 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 28 total
  • MANE Select transcript: NM_181553

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19174
Approved symbolCMTM3
NameCKLF like MARVEL transmembrane domain containing 3
Location16q22.1
Locus typegene with protein product
StatusApproved
AliasesFLJ31762, BNAS2
Ensembl geneENSG00000140931
Ensembl biotypeprotein_coding
OMIM607886
Entrez123920

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 23 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000361909, ENST00000424011, ENST00000460097, ENST00000562357, ENST00000562707, ENST00000563672, ENST00000564060, ENST00000564247, ENST00000565003, ENST00000565666, ENST00000565922, ENST00000566121, ENST00000566756, ENST00000567572, ENST00000568477, ENST00000885751, ENST00000885752, ENST00000885753, ENST00000885754, ENST00000885755, ENST00000918764, ENST00000918765, ENST00000967212, ENST00000967213, ENST00000967214

RefSeq mRNA: 4 — MANE Select: NM_181553 NM_001363918, NM_001363923, NM_144601, NM_181553

CCDS: CCDS10815

Canonical transcript exons

ENST00000567572 — 5 exons

ExonStartEnd
ENSE000009456276660943566609530
ENSE000015175186661260966613887
ENSE000025878336660470466604952
ENSE000034611826660988366610003
ENSE000035334636660830966608464

Expression profiles

Bgee: expression breadth ubiquitous, 237 present calls, max score 96.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.3917 / max 238.5133, expressed in 1786 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
15452516.62171709
15452615.46491715
1545240.8418317
1545280.6653428
1545270.4111232
1545230.3870188

Top tissues by expression

251 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009496.91gold quality
leukocyteCL:000073895.62gold quality
monocyteCL:000057695.51gold quality
right testisUBERON:000453495.48gold quality
stromal cell of endometriumCL:000225595.31gold quality
left testisUBERON:000453395.22gold quality
gall bladderUBERON:000211094.83gold quality
testisUBERON:000047394.14gold quality
bloodUBERON:000017894.00gold quality
right lungUBERON:000216793.81gold quality
endocervixUBERON:000045893.36gold quality
deciduaUBERON:000245093.31gold quality
right ovaryUBERON:000211893.17gold quality
subcutaneous adipose tissueUBERON:000219092.89gold quality
omental fat padUBERON:001041492.84gold quality
peritoneumUBERON:000235892.81gold quality
adipose tissue of abdominal regionUBERON:000780892.59gold quality
tibial nerveUBERON:000132392.50gold quality
left ovaryUBERON:000211992.36gold quality
vermiform appendixUBERON:000115492.25gold quality
upper lobe of left lungUBERON:000895291.99gold quality
left uterine tubeUBERON:000130391.96gold quality
lymph nodeUBERON:000002991.70gold quality
amniotic fluidUBERON:000017391.61gold quality
right coronary arteryUBERON:000162591.56gold quality
pericardiumUBERON:000240791.56gold quality
adipose tissueUBERON:000101391.52gold quality
cartilage tissueUBERON:000241891.48gold quality
ectocervixUBERON:001224991.23gold quality
mucosa of stomachUBERON:000119991.21gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-8271yes14.98
E-ANND-3yes9.95
E-GEOD-100618no220.37
E-CURD-112no2.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

65 targeting CMTM3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-311999.9271.342390
HSA-MIR-464899.9167.00710
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-629-3P99.8567.991875
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-4639-5P99.8167.371028
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-197699.7465.481127
HSA-MIR-29B-2-5P99.6768.981726
HSA-MIR-317599.6566.302031
HSA-MIR-4743-3P99.6268.122095
HSA-MIR-24-3P99.5969.971934
HSA-MIR-431699.3765.751360
HSA-MIR-377-3P99.3770.181905
HSA-MIR-135A-5P99.3671.851601
HSA-MIR-135B-5P99.3671.631613
HSA-MIR-3606-5P99.3169.671168
HSA-MIR-450599.2767.812678
HSA-MIR-3064-5P99.2666.131497
HSA-MIR-3085-3P99.2666.161490
HSA-MIR-6504-5P99.2665.951487

Literature-anchored findings (GeneRIF, showing 17)

  • Bioinformatics based on CKLF2 cDNA and protein sequences in combination with experimental validation identified CKLFSF1-8 gene clusters, between the SCY and the TM4SF gene families. The 8 family members were cloned and characterized. (PMID:12782130)
  • CMTM3/CKLFSF3 is an evolutionarily conserved gene that may have important roles in the male reproductive system and immune system. (PMID:17002874)
  • CMTM3 inhibits prostate-specific antigen expression at both mRNA and protein levels with no obvious influence on androgen receptor expression. (PMID:18402773)
  • CMTM3 is significantly down-regulated in clear cell renal cell carcinoma and exerts remarkable tumor-suppressive functions (PMID:23907292)
  • Peritoneal disseminated metastases were significantly suppressed by CMTM3. (PMID:24131472)
  • CMTM1 and 3 are priority targets in glioblastomas. First insights into signalling of these two genes that might be conveyed by growth factor receptor, Src family kinase and WNT activation was presented. (PMID:25931111)
  • Low expression of CMTM3 was associated with metastasis and recurrence of oral squamous cell carcinoma. (PMID:25946973)
  • Reduced expression of CMTM3 is associated with prostate cancer. (PMID:25990505)
  • this study demonstrates that knockdown of CMTM3 promotes the metastasis of gastric cancer through the STAT3/Twist1/EMT pathway (PMID:27121055)
  • identified CMTM3 as a novel secretory protein released via exosomes in the prostate (PMID:27125975)
  • 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 (PMID:27521994)
  • Overexpression of CMTM3 attenuated the tumor growth of hepatocellular carcinoma. (PMID:27629543)
  • CMTM3 decreases EGFR expression, facilitates EGFR degradation, and inhibits the EGF-mediated tumorigenicity of gastric cancer cells by enhancing Rab5 activity. (PMID:27867015)
  • CMTM3 mediates cell-cell adhesion at adherens junctions and contributes to the control of vascular sprouting by regulation VE-cadherin turnover. (PMID:28428220)
  • CMTM3 was significantly hypermethylated in colorectal cancer tissues when compared with adjacent normal colorectal tissues. (PMID:28782576)
  • CMTM3 exhibited a lower expression pattern in gastric cancer tissues.MiR-135b-5p promotes gastric cancer progression by targeting CMTM3. (PMID:29345297)
  • Familial hypereosinophilia associated with eosinophilic gastrointestinal symptoms in individuals with a missense mutation in CKLF-like MARVEL transmembrane domain containing 3. (PMID:34048099)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocmtm3ENSDARG00000008811
mus_musculusCmtm3ENSMUSG00000031875
rattus_norvegicusCmtm3ENSRNOG00000010691
caenorhabditis_elegansF28H1.4WBGENE00017909
caenorhabditis_elegansF47B3.3WBGENE00018527

Paralogs (14): CMTM1 (ENSG00000089505), CMTM6 (ENSG00000091317), PLP2 (ENSG00000102007), PLLP (ENSG00000102934), CMTM2 (ENSG00000140932), MALL (ENSG00000144063), MAL2 (ENSG00000147676), CMTM7 (ENSG00000153551), MARVELD1 (ENSG00000155254), CMTM5 (ENSG00000166091), CMTM8 (ENSG00000170293), MAL (ENSG00000172005), CMTM4 (ENSG00000183723), CKLF (ENSG00000217555)

Protein

Protein identifiers

CKLF-like MARVEL transmembrane domain-containing protein 3Q96MX0 (reviewed: Q96MX0)

Alternative names: Chemokine-like factor superfamily member 3

All UniProt accessions (8): Q96MX0, H3BN06, H3BU39, H3BUD5, I3L3C2, I3L540, J3KSM1, J3KSR6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

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

Similarity. Belongs to the chemokine-like factor family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96MX0-11yes
Q96MX0-22

RefSeq proteins (4): NP_001350847, NP_001350852, NP_653202, NP_853531* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008253MarvelDomain
IPR050578MARVEL-CKLF_proteinsFamily

Pfam: PF01284

UniProt features (9 total): transmembrane region 3, splice variant 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96MX0-F179.990.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 191 (showing top): GOBP_REGULATION_OF_B_CELL_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, chr16q22, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_TAXIS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN, GOBP_POSITIVE_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_BLASTOCYST_DEVELOPMENT, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, GOMF_CYTOKINE_ACTIVITY, GOBP_EMBRYO_DEVELOPMENT

GO Biological Process (4): blastocyst hatching (GO:0001835), chemotaxis (GO:0006935), positive regulation of B cell receptor signaling pathway (GO:0050861), signal transduction (GO:0007165)

GO Molecular Function (2): cytokine activity (GO:0005125), protein binding (GO:0005515)

GO Cellular Component (6): obsolete extracellular space (GO:0005615), cytosol (GO:0005829), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), nuclear membrane (GO:0031965), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cytoplasm2
blastocyst development1
hatching1
response to chemical1
taxis1
B cell receptor signaling pathway1
regulation of B cell receptor signaling pathway1
positive regulation of antigen receptor-mediated signaling pathway1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
receptor ligand activity1
binding1
intracellular vesicle1
nucleus1
nuclear envelope1
organelle membrane1
intracellular anatomical structure1

Protein interactions and networks

STRING

626 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CMTM3CMTM1Q8IZ96975
CMTM3CMTM2Q8TAZ6968
CMTM3CKLFQ9UBR5967
CMTM3CMTM4Q8IZR5966
CMTM3CMTM7Q96FZ5887
CMTM3CMTM8Q8IZV2761
CMTM3CMTM6Q9NX76750
CMTM3SF3B3Q15393496
CMTM3KYNUQ16719474
CMTM3BEAN1Q3B7T3443
CMTM3ZNF354AO60765433
CMTM3DCTPP1Q9H773427
CMTM3NSA2O95478422
CMTM3UBAC2Q8NBM4416
CMTM3SNRPFP62306410
CMTM3PRRG1O14668410

IntAct

70 interactions, top by confidence:

ABTypeScore
CMTM3MOB3Cpsi-mi:“MI:0915”(physical association)0.560
CMTM3MOB1Apsi-mi:“MI:0915”(physical association)0.560
MOB3CCMTM3psi-mi:“MI:0915”(physical association)0.560
MOB1ACMTM3psi-mi:“MI:0915”(physical association)0.560
CMTM3RETREG3psi-mi:“MI:0915”(physical association)0.560
CMTM3psi-mi:“MI:0915”(physical association)0.560
LRRC59CMTM3psi-mi:“MI:0915”(physical association)0.560
CREB3L1CMTM3psi-mi:“MI:0915”(physical association)0.560
IKBIPCMTM3psi-mi:“MI:0915”(physical association)0.560
GJB1CMTM3psi-mi:“MI:0915”(physical association)0.560
LEUTXCMTM3psi-mi:“MI:0915”(physical association)0.560
ARL13BCMTM3psi-mi:“MI:0915”(physical association)0.560
RETREG3CMTM3psi-mi:“MI:0915”(physical association)0.560
CMTM3STMN4psi-mi:“MI:0915”(physical association)0.560
APOA5CMTM3psi-mi:“MI:0915”(physical association)0.560
IL10RACMTM3psi-mi:“MI:0915”(physical association)0.560
CMTM3REEP4psi-mi:“MI:0915”(physical association)0.560
SYT2CMTM3psi-mi:“MI:0915”(physical association)0.560
HSD17B11CMTM3psi-mi:“MI:0915”(physical association)0.560
CMTM3ELOVL4psi-mi:“MI:0915”(physical association)0.560
SLC10A1CMTM3psi-mi:“MI:0915”(physical association)0.560
MFSD14BCMTM3psi-mi:“MI:0915”(physical association)0.560
AQP6CMTM3psi-mi:“MI:0915”(physical association)0.560
MRM1CMTM3psi-mi:“MI:0915”(physical association)0.560
CMTM3F13A1psi-mi:“MI:0915”(physical association)0.560

BioGRID (31): CMTM3 (Two-hybrid), MOB3C (Two-hybrid), CMTM3 (Two-hybrid), CMTM3 (Negative Genetic), CMTM3 (Synthetic Lethality), CMTM3 (Two-hybrid), CMTM3 (Two-hybrid), CMTM3 (Two-hybrid), CMTM3 (Two-hybrid), CMTM3 (Two-hybrid), CMTM3 (Two-hybrid), CMTM3 (Two-hybrid), CMTM3 (Two-hybrid), FAM134C (Two-hybrid), SYT2 (Two-hybrid)

ESM2 similar proteins: A2VE13, A6QNL6, B6ID01, O09198, P16646, P20274, P21145, P25094, P54825, P55344, P56563, Q01453, Q04941, Q17R16, Q1RMP9, Q28296, Q2TA01, Q3ZBY0, Q4PNJ2, Q5BJS2, Q5R6H1, Q5RAI2, Q5RAZ3, Q5U1W4, Q5U4E0, Q5VXU1, Q64349, Q6WL85, Q6Y1E2, Q7TSY2, Q7Z7J7, Q86UP9, Q8BI08, Q8BM86, Q8IZV2, Q91XQ6, Q95MN6, Q969L2, Q96FZ5, Q96MX0

Diamond homologs: Q96MX0, Q99LJ5, Q9D6G9, Q9R1Q7, Q04941, Q6P742, Q6Y1E2, Q95MN6, Q96DZ9, Q28597

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

28 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance23
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1262 predictions. Top by Δscore:

VariantEffectΔscore
16:66609433:A:AGacceptor_gain1.0000
16:66609433:AG:Aacceptor_gain1.0000
16:66609434:G:GGacceptor_gain1.0000
16:66609434:GG:Gacceptor_gain1.0000
16:66609528:GGG:Gdonor_gain1.0000
16:66609529:GG:Gdonor_gain1.0000
16:66609529:GGG:Gdonor_gain1.0000
16:66609530:GG:Gdonor_gain1.0000
16:66609531:G:GGdonor_gain1.0000
16:66609531:GTGAG:Gdonor_loss1.0000
16:66609532:T:Gdonor_loss1.0000
16:66609877:CCACA:Cacceptor_loss1.0000
16:66609878:CACA:Cacceptor_loss1.0000
16:66609879:ACAG:Aacceptor_loss1.0000
16:66609880:CA:Cacceptor_loss1.0000
16:66609881:A:ACacceptor_loss1.0000
16:66609882:GGT:Gacceptor_gain1.0000
16:66609999:AGAAG:Adonor_gain1.0000
16:66610000:GAAG:Gdonor_gain1.0000
16:66610000:GAAGG:Gdonor_gain1.0000
16:66610001:AAG:Adonor_gain1.0000
16:66610002:AG:Adonor_gain1.0000
16:66610002:AGGTA:Adonor_loss1.0000
16:66610003:GG:Gdonor_gain1.0000
16:66610003:GGTA:Gdonor_loss1.0000
16:66610004:G:GAdonor_loss1.0000
16:66610004:G:GGdonor_gain1.0000
16:66604949:GTCG:Gdonor_gain0.9900
16:66607693:GGCAC:Gdonor_gain0.9900
16:66608307:AG:Aacceptor_gain0.9900

AlphaMissense

1178 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:66609914:C:AA144E0.981
16:66609910:T:CF143L0.979
16:66609912:T:AF143L0.979
16:66609912:T:GF143L0.979
16:66609890:G:AG136D0.977
16:66609457:C:AA109E0.975
16:66608333:T:CC58R0.974
16:66609526:C:AA132D0.974
16:66609449:T:GC106W0.971
16:66609899:C:AA139D0.969
16:66604949:G:CE48D0.967
16:66604949:G:TE48D0.967
16:66609908:T:AV142E0.967
16:66604929:G:CG42R0.966
16:66609889:G:CG136R0.965
16:66609438:T:CF103L0.963
16:66609440:C:AF103L0.963
16:66609440:C:GF103L0.963
16:66609913:G:CA144P0.961
16:66608309:G:CG50R0.960
16:66609529:G:AG133E0.960
16:66609481:C:AS117Y0.958
16:66608373:C:AP71H0.956
16:66609447:T:CC106R0.956
16:66608373:C:GP71R0.955
16:66609481:C:TS117F0.955
16:66609460:C:AA110D0.954
16:66604928:A:CK41N0.953
16:66604928:A:TK41N0.953
16:66609925:T:GY148D0.952

dbSNP variants (sampled 300 via entrez): RS1000200038 (16:66605063 C>A,G,T), RS1000626248 (16:66611219 G>A), RS1000739094 (16:66606618 T>C), RS1000830569 (16:66613833 G>A), RS1000982628 (16:66606349 G>C), RS1001393590 (16:66611536 G>A), RS1001396513 (16:66602353 T>C), RS1001465762 (16:66611935 C>T), RS1001481110 (16:66608041 T>A), RS1001547184 (16:66610744 T>C,G), RS1001645509 (16:66605879 G>A,C), RS1001904161 (16:66606945 G>A), RS1001975223 (16:66605601 G>A), RS1002377789 (16:66607176 C>G), RS1002785603 (16:66613438 G>A,C)

Disease associations

OMIM: gene MIM:607886 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

43 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, increases expression, affects cotreatment3
Benzo(a)pyreneincreases expression, increases methylation3
Tetrachlorodibenzodioxinincreases expression3
sodium arsenitedecreases expression, increases abundance, increases expression2
Arsenicincreases expression, decreases expression, increases abundance2
Estradiolaffects cotreatment, decreases expression, increases expression2
Valproic Aciddecreases expression, increases methylation, affects expression2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
tris(2-butoxyethyl) phosphateaffects expression1
beta-lapachoneincreases expression1
cobaltous chloridedecreases expression1
zinc chromatedecreases expression, increases abundance1
manganese chlorideincreases abundance, decreases expression1
potassium chromate(VI)decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression, increases abundance1
K 7174increases expression1
bisphenol Sdecreases methylation1
Air Pollutantsaffects expression, increases abundance1
Ethanolaffects cotreatment, increases abundance, increases expression1
Calcitrioldecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Gasolineaffects cotreatment, increases abundance, increases expression1
Indomethacinaffects cotreatment, increases expression1
Manganesedecreases expression, increases abundance1
Ozoneaffects expression, increases abundance1
Polycyclic Aromatic Hydrocarbonsincreases abundance, increases expression, affects cotreatment1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.