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CEACAM20

gene
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Also known as UNQ9366

Summary

CEACAM20 (CEA cell adhesion molecule 20, HGNC:24879) is a protein-coding gene on chromosome 19q13.31, encoding Cell adhesion molecule CEACAM20 (Q6UY09). Together with the tyrosine-protein kinase SYK, enhances production of the cytokine CXCL8/IL-8 via the NFKB pathway and may thus have a role in the intestinal immune response.

Predicted to enable protein tyrosine kinase binding activity. Predicted to be involved in regulation of immune system process and signal transduction. Predicted to be located in apical plasma membrane and microvillus membrane. Predicted to be active in cell surface and plasma membrane.

Source: NCBI Gene 125931 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 82 total
  • GTEx eGene: eQTL in 4 tissues, sQTL in 0 (q < 0.05)
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.05 (unconstrained)
  • MANE Select transcript: NM_001102597
  • Notable: 82 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24879
Approved symbolCEACAM20
NameCEA cell adhesion molecule 20
Location19q13.31
Locus typegene with protein product
StatusApproved
AliasesUNQ9366
Ensembl geneENSG00000273777
Ensembl biotypeprotein_coding
Entrez125931

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

MANE Select: ENST00000614924

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 5

ENST00000614924, ENST00000611497, ENST00000614577, ENST00000620096, ENST00000621342, ENST00001142114

RefSeq mRNA: 4 — MANE Select: NM_001102597 NM_001102597, NM_001102598, NM_001102599, NM_001102600

CCDS: CCDS74390, CCDS74391, CCDS74392, CCDS74393

Canonical transcript exons

ENST00000614924 — 12 exons

ExonStartEnd
ENSE000037183464452047444520752
ENSE000037187464451163744511672
ENSE000037199734451286844512953
ENSE000037238044452263444522912
ENSE000037264584451201744512078
ENSE000037384954452510144525244
ENSE000037393284452398644524261
ENSE000037402284451317244513289
ENSE000037414274451103044511155
ENSE000037474264450615944506214
ENSE000037520944451694644517224
ENSE000038904884452945844529675

Expression profiles

Bgee: expression breadth broad, 36 present calls, max score 92.71.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1182 / max 146.3176, expressed in 9 samples.

Highest expression (Bgee): duodenum, small intestine, small intestine Peyer’s patch, gall bladder, prostate gland.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CEACAM20 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 4 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

4 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Testiseqtl9.9e-06+0.4219:44536461:G:A
Adrenal Glandeqtl7.1e-03+1.5819:44037780:C:T
Lungeqtl1.7e-02-0.2519:44606802:C:G
Livereqtl2.8e-02-0.3819:44738850:G:A

FANTOM5 promoters

2 alternative TSS:

Promoter IDTPM avgSamples expressed
1813980.10617
1813990.01213

Top tissues by expression

showing 100 of 116 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
duodenumUBERON:000211492.71gold quality
small intestineUBERON:000210878.36gold quality
small intestine Peyer’s patchUBERON:000345477.92gold quality
gall bladderUBERON:000211055.78gold quality
prostate glandUBERON:000236748.10gold quality
smooth muscle tissueUBERON:000113548.00gold quality
right lobe of liverUBERON:000111446.94gold quality
liverUBERON:000210745.47gold quality
intestineUBERON:000016044.66gold quality
right adrenal gland cortexUBERON:003582744.57gold quality
placentaUBERON:000198743.37gold quality
vermiform appendixUBERON:000115442.11silver quality
colonic epitheliumUBERON:000039741.37gold quality
right adrenal glandUBERON:000123340.42gold quality
bone marrow cellCL:000209240.27gold quality
stromal cell of endometriumCL:000225539.49gold quality
lower esophagus mucosaUBERON:003583438.72gold quality
rectumUBERON:000105238.71silver quality
left testisUBERON:000453338.54gold quality
right testisUBERON:000453438.39gold quality
testisUBERON:000047338.35gold quality
left adrenal gland cortexUBERON:003582537.67gold quality
bone marrowUBERON:000237137.48gold quality
granulocyteCL:000009437.45gold quality
muscle tissueUBERON:000238537.38gold quality
left adrenal glandUBERON:000123437.35silver quality
adrenal glandUBERON:000236936.99gold quality
ventricular zoneUBERON:000305336.48gold quality
cortical plateUBERON:000534336.47gold quality
apex of heartUBERON:000209836.25gold quality
tonsilUBERON:000237236.07gold quality
sural nerveUBERON:001548835.99gold quality
ganglionic eminenceUBERON:000402335.49gold quality
skeletal muscle tissueUBERON:000113434.60gold quality
mucosa of stomachUBERON:000119934.48gold quality
urinary bladderUBERON:000125533.58silver quality
transverse colonUBERON:000115733.45gold quality
leukocyteCL:000073832.59gold quality
monocyteCL:000057632.44gold quality
cortex of kidneyUBERON:000122532.22gold quality
hindlimb stylopod muscleUBERON:000425232.15gold quality
colonUBERON:000115532.12gold quality
prefrontal cortexUBERON:000045130.49gold quality
lymph nodeUBERON:000002930.29gold quality
adrenal tissueUBERON:001830329.97gold quality
right uterine tubeUBERON:000130229.93gold quality
fallopian tubeUBERON:000388929.89silver quality
endometriumUBERON:000129529.63gold quality
myometriumUBERON:000129629.39gold quality
uterine cervixUBERON:000000229.05gold quality
multicellular organismUBERON:000046828.76gold quality
fundus of stomachUBERON:000116028.73gold quality
endocervixUBERON:000045828.54gold quality
right hemisphere of cerebellumUBERON:001489028.19gold quality
kidneyUBERON:000211328.07gold quality
islet of LangerhansUBERON:000000628.03gold quality
pituitary glandUBERON:000000727.79silver quality
cerebellar hemisphereUBERON:000224527.51gold quality
cerebellar cortexUBERON:000212927.44gold quality
pancreasUBERON:000126427.43gold quality
right atrium auricular regionUBERON:000663127.41gold quality
cerebellumUBERON:000203727.40gold quality
olfactory segment of nasal mucosaUBERON:000538627.39gold quality
ectocervixUBERON:001224927.25gold quality
calcaneal tendonUBERON:000370126.89gold quality
frontal cortexUBERON:000187026.75gold quality
adenohypophysisUBERON:000219626.57gold quality
tibial nerveUBERON:000132326.56gold quality
body of pancreasUBERON:000115026.15gold quality
right lungUBERON:000216726.07gold quality
body of uterusUBERON:000985326.04gold quality
muscle layer of sigmoid colonUBERON:003580525.81silver quality
skin of legUBERON:000151125.49gold quality
tibial arteryUBERON:000761025.48gold quality
popliteal arteryUBERON:000225025.43gold quality
Ammon’s hornUBERON:000195425.30gold quality
cerebral cortexUBERON:000095625.26gold quality
esophagusUBERON:000104325.18gold quality
esophagus mucosaUBERON:000246925.08gold quality
lower esophagusUBERON:001347325.01gold quality
lower esophagus muscularis layerUBERON:003583325.00gold quality
zone of skinUBERON:000001424.96gold quality
spleenUBERON:000210624.92gold quality
primary visual cortexUBERON:000243624.61gold quality
descending thoracic aortaUBERON:000234524.58gold quality
metanephros cortexUBERON:001053324.56gold quality
left uterine tubeUBERON:000130324.43gold quality
superior frontal gyrusUBERON:000266124.08gold quality
C1 segment of cervical spinal cordUBERON:000646924.06gold quality
ascending aortaUBERON:000149624.05gold quality
thoracic aortaUBERON:000151524.04gold quality
thyroid glandUBERON:000204624.01gold quality
right ovaryUBERON:000211823.98gold quality
left lobe of thyroid glandUBERON:000112023.79gold quality
skin of abdomenUBERON:000141623.74gold quality
substantia nigraUBERON:000203823.58gold quality
dorsolateral prefrontal cortexUBERON:000983423.58gold quality
esophagogastric junction muscularis propriaUBERON:003584123.50gold quality
temporal lobeUBERON:000187123.23gold quality
ovaryUBERON:000099223.17gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.09
E-ENAD-17no45.20

HPA expression

RNA tissue specificity: Tissue enriched

37 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPM
Small intestinetissue35.6
Duodenumtissue35.2
Prostatetissue7.9
Cerebellumtissue1.5
Olfactory bulbtissue1.3
Cerebral cortextissue1.1
Retrosplenial and cingulate cortextissue1.1
Retrosplenial cortextissue1.1
Occipital cortextissue1.1
Insular cortextissue1.1
Prefrontal cortextissue1.0
Motor cortextissue1.0
Basal gangliatissue1.0
Amygdalatissue1.0
Corpus callosumtissue1.0
Hippocampal formationtissue1.0
Entorhinal cortextissue1.0
Somatosensory cortextissue1.0
Temporal cortextissue1.0
Ventral forebraintissue0.9
Septumtissue0.9
Putamentissue0.8
Periaqueductal graytissue0.8
Medulla oblongatatissue0.7
Hypothalamustissue0.7
Superior colliculitissue0.7
Substantia nigratissue0.7
Gallbladdertissue0.7
Spinal cordtissue0.7
Ponstissue0.6
Midbraintissue0.6
Thalamustissue0.6
Testistissue0.4
Smooth muscletissue0.3
Placentatissue0.1
Livertissue0.1
Tonsiltissue0.1

Brain sub-regions (HPA Brain Atlas): detected in 9; highest nTPM — Subiculum (1.0), White matter (1.0), Dorsal hippocampus (0.9), Ventral hippocampus (0.9), Dorsal spinal cord (0.7).

Regulation

Is transcription factor: no

Functional genomics

gnomAD constraint: pLI 1.97e-14, LOEUF 1.05, missense Z 0.991 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000614924 — one region, missense o/e 0.93.

Literature-anchored findings (GeneRIF, showing 2)

  • conclude that CEACAM20 and CEACAM1 not only mark the lumina of adult prostate tissue but also play a critical role in the vitro generation of prostate organoids (PMID:23358633)
  • tyrosine phosphorylation of CEACAM20 likely promotes phagocytic activity (PMID:28659570)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosi:dkeyp-97a10.3ENSDARG00000104656
danio_reriosi:dkey-11o1.7ENSDARG00000105324
mus_musculusCeacam20ENSMUSG00000070777
rattus_norvegicusCeacam20ENSRNOG00000019260

Paralogs (24): CEACAM21 (ENSG00000007129), CEACAM7 (ENSG00000007306), CEACAM1 (ENSG00000079385), CEACAM6 (ENSG00000086548), CEACAM4 (ENSG00000105352), CEACAM5 (ENSG00000105388), PSG8 (ENSG00000124467), CEACAM8 (ENSG00000124469), HEPACAM (ENSG00000165478), PSG6 (ENSG00000170848), CEACAM3 (ENSG00000170956), PSG9 (ENSG00000183668), CEACAM19 (ENSG00000186567), HEPACAM2 (ENSG00000188175), PSG5 (ENSG00000204941), CEACAM18 (ENSG00000213822), CEACAM16 (ENSG00000213892), VSTM5 (ENSG00000214376), PSG3 (ENSG00000221826), PSG7 (ENSG00000221878), PSG1 (ENSG00000231924), PSG2 (ENSG00000242221), PSG11 (ENSG00000243130), PSG4 (ENSG00000243137)

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
ZNF180protein-coding7733
ZNF229protein-coding7772
MIR4531ncRNA100616355
IGSF23protein-coding147710
CEACAM19protein-coding56971
PVRprotein-coding5817
ZNF285protein-coding26974

Protein

Protein identifiers

Cell adhesion molecule CEACAM20 — Q6UY09 (reviewed: Q6UY09)

Alternative names: Carcinoembryonic antigen-related cell adhesion molecule 20

All UniProt accessions (1): Q6UY09

UniProt curated annotations — full annotation on UniProt →

Function. Together with the tyrosine-protein kinase SYK, enhances production of the cytokine CXCL8/IL-8 via the NFKB pathway and may thus have a role in the intestinal immune response.

Subunit / interactions. Interacts (via extracellular domain) with PTPRH (via extracellular domain); the interaction dephosphorylates CEACAM20. Interacts (phosphorylated form) with SYK (via SH2 domains); the interaction further enhances CEACAM20 phosphorylation.

Subcellular location. Cell projection. Microvillus membrane. Apical cell membrane.

Post-translational modifications. Phosphorylated on tyrosine residues by SYK, SRC and FYN in vitro.

Similarity. Belongs to the immunoglobulin superfamily. CEA family.

Isoforms (5)

UniProt IDNamesCanonical?
Q6UY09-11yes
Q6UY09-22
Q6UY09-33
Q6UY09-44
Q6UY09-55

RefSeq proteins (4): NP_001096067, NP_001096068, NP_001096069, NP_001096070 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR052598IgSF_CEA-relatedFamily

Pfam: PF13927

UniProt features (37 total): glycosylation site 7, sequence variant 7, domain 4, disulfide bond 3, splice variant 3, region of interest 2, compositionally biased region 2, modified residue 2, topological domain 2, sequence conflict 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6UY09-F173.870.52

Human Protein Atlas

Protein class: Predicted membrane proteins, UniProt - Evidence at transcript level

Protein evidence: Evidence at protein level

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2)

TypePositions
Phosphotyrosine578, 589

Disulfide bonds (3)

TypePositions
Disulfide bond90–138, 276–324, 375–416

Glycosylation sites (7)

TypePositions
N-linked (glcnac…) asparagine96, 105, 280, 306, 317, 368, 415

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 40 (showing top): GOCC_CELL_SURFACE, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, SHEPARD_BMYB_MORPHOLINO_DN, GOBP_CYTOKINE_PRODUCTION, GOCC_APICAL_PLASMA_MEMBRANE, AACTTT_UNKNOWN, GOBP_POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOCC_CELL_PROJECTION_MEMBRANE, GOCC_APICAL_PART_OF_CELL, GOCC_MICROVILLUS, GOCC_MICROVILLUS_MEMBRANE, GOCC_PLASMA_MEMBRANE_REGION, GOCC_ACTIN_BASED_CELL_PROJECTION, GOBP_RESPONSE_TO_BACTERIUM, GOMF_KINASE_BINDING

GO Biological Process (5): positive regulation of cytokine production (GO:0001819), immune system process (GO:0002376), regulation of immune system process (GO:0002682), signal transduction (GO:0007165), response to bacterium (GO:0009617)

GO Molecular Function (1): protein tyrosine kinase binding (GO:1990782)

GO Cellular Component (4): plasma membrane (GO:0005886), cell surface (GO:0009986), apical plasma membrane (GO:0016324), microvillus membrane (GO:0031528)

GO top-level categories

21 GO namespaces:

CategoryTerms
cytokine production1
regulation of cytokine production1
positive regulation of gene expression1
positive regulation of multicellular organismal process1
biological_process1
immune system process1
regulation of biological process1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
response to other organism1
protein kinase binding1
membrane1
cell periphery1
cellular anatomical structure1
apical part of cell1
plasma membrane region1
microvillus1
cell projection membrane1

Protein interactions and networks

STRING

showing 15 of 232 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
CEACAM20CEACAM19Q7Z692746
CEACAM20CEACAM4O75871610
CEACAM20CEACAM3P40198495
CEACAM20PRAMEF19Q5SWL8419
CEACAM20ZNF23P17027400
CEACAM20A0A087WTH5A0A087WTH5359
CEACAM20OR10G2Q8NGC3345
CEACAM20CEACAM18A8MTB9337
CEACAM20SMIM11P58511315
CEACAM20SPDYE3A6NKU9314
CEACAM20LHFPL1Q86WI0308
CEACAM20TRERF1Q96PN7295
CEACAM20PTPRHQ9HD43273
CEACAM20RGPD1P0C839270
CEACAM20CEACAM21Q3KPI0262

Disease & clinical

Genetic variants

Variant evidence for CEACAM20: 82 ClinVar records (0 pathogenic / likely pathogenic); 5 GWAS associations.

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance75
Likely benign4
Benign0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 34 predictions of 897):

Position(s)EffectΔscoreSites
19:44511594donor_gain1.0000
19:44512955acceptor_loss1.0000
19:44511028–44511029donor_loss0.99005
19:44511156–44511157acceptor_loss0.99004
19:44512015–44512016donor_loss0.99005
19:44512079–44512080acceptor_loss0.99004
19:44512866–44512867donor_loss0.99005
19:44512954–44512955acceptor_loss0.99002
19:44513290–44513291acceptor_loss0.99006
19:44524262acceptor_gain0.9900

AlphaMissense

437 missense substitutions predicted likely pathogenic (of 3,866 scored), across 152 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
D13280.8850.948
W28770.9680.995
C32470.9630.981
C27670.9610.981
C41670.9600.986
W38770.9560.994
C37570.9500.982
W10170.9280.987
C13870.9170.976
C9070.8890.945
W20170.8670.968
C23070.8580.941
N42070.8520.972
D31870.8070.892
N23470.7810.949
S33560.8800.966
P34660.8750.961
G34560.8650.963
S14960.8220.948
V15660.8000.923

HPA cancer prognostics

RNA cancer specificity: Cancer enriched (Prostate Adenocarcinoma)

Disease associations

OMIM: gene `` | disease phenotypes:

GWAS associations

5 associations:

StudyTraitp-value
GCST007320_18Alzheimer’s disease or family history of Alzheimer’s disease1e-12
GCST005952_8Body mass index (age>50)9e-12
GCST005950_15Body mass index x sex x age interaction (4df test)2e-10
GCST005954_4Body mass index x age interaction2e-7
GCST005951_66Body mass index1e-6

EFO canonical traits (from GWAS)

4 canonical traits:

EFO IDTrait name
EFO:0004340body mass index
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0009268family history of Alzheimer’s disease

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression2
Aflatoxin B1decreases methylation, increases methylation2
methyleugenoldecreases expression1
bisphenol Aaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Indomethacinaffects cotreatment, decreases expression1
N-Nitrosopyrrolidinedecreases expression1
Thiramincreases expression1
Urethaneincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, decreases expression1
Cadmium Chlorideincreases expression1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

12 trials:

NCTPhaseStatusTitle
NCT03414970Phase 3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344Phase 2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999Phase 2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364Phase 1/2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855Phase 1/2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908Early Phase 1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041Early Phase 1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT07628634Early Phase 1RECRUITINGFeasibility Study on the Effect of a Methionine-Reduced Diet on Serum Levels in Pts w/ Solid Tumors
NCT01208974Not specifiedCOMPLETEDNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery

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