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CEACAM4

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Summary

CEACAM4 (CEA cell adhesion molecule 4, HGNC:1816) is a protein-coding gene on chromosome 19q13.2, encoding Cell adhesion molecule CEACAM4 (O75871). Granulocyte orphan receptor that acts as an trigger efficient phagocytosis of attached particles.

Predicted to enable protein tyrosine kinase binding activity. Involved in phagocytosis. Predicted to be located in membrane. Predicted to be active in cell surface and plasma membrane.

Source: NCBI Gene 1089 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 47 total
  • GTEx eGene: eQTL in 22 tissues, sQTL in 3 (q < 0.05)
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.45 (unconstrained)
  • MANE Select transcript: NM_001817

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1816
Approved symbolCEACAM4
NameCEA cell adhesion molecule 4
Location19q13.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000105352
Ensembl biotypeprotein_coding
OMIM619159
Entrez1089

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

MANE Select: ENST00000221954

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 2

ENST00000221954, ENST00000472081, ENST00000600925, ENST00000902906, ENST00001028485, ENST00001093480, ENST00001093481, ENST00001143378

RefSeq mRNA: 4 — MANE Select: NM_001817 NM_001362492, NM_001362493, NM_001362495, NM_001817

CCDS: CCDS33033

Canonical transcript exons

ENST00000221954 — 7 exons

ExonStartEnd
ENSE000007085454162560141625960
ENSE000008424604161967041619711
ENSE000008424614162021141620242
ENSE000013228064161901541619395
ENSE000024939264162165141621768
ENSE000025143444162057541620627
ENSE000035549114162690041627074

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 95.65.

FANTOM5 (CAGE): breadth broad, TPM avg 3.1596 / max 431.5855, expressed in 241 samples.

Highest expression (Bgee): blood, monocyte, spleen, leukocyte, granulocyte.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CEACAM4 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 22 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 25 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Whole Bloodsqtl4.9e-68+0.8919:41620075:C:T
Whole Bloodeqtl8.9e-33-0.2119:41619287:C:T
Nerve Tibialeqtl1.2e-13-0.2519:41609565:A:G
Artery Tibialeqtl2.1e-12-0.2419:41621829:A:G
Spleensqtl1.0e-10+0.7919:41618000:A:AACCTGTGGCAGTGGCAGAACACTCTTGGG
Lungeqtl7.0e-07-0.1319:41609565:A:G
Esophagus Mucosaeqtl1.1e-06-0.1819:41609815:C:G
Pancreaseqtl1.5e-04+0.9419:41597766:G:A
Breast Mammary Tissueeqtl2.8e-04-0.1919:41632519:T:C
Spleeneqtl4.8e-04-0.7419:41664392:C:A
Adrenal Glandeqtl6.9e-04-0.3819:41624402:A:G
Skin Sun Exposed Lower legeqtl7.6e-04-0.1519:41619287:C:T
Brain Putamen basal gangliaeqtl1.3e-03-1.5019:40670091:C:T
Esophagus Musculariseqtl1.3e-03-0.2019:41609766:A:G
Adipose Visceral Omentumeqtl2.7e-03-0.1119:41609766:A:G
Lungsqtl5.3e-03-0.3719:41619287:C:T
Colon Transverseeqtl5.9e-03-0.1819:41609766:A:G
Esophagus Gastroesophageal Junctioneqtl7.9e-03-0.2119:41610711:A:G
Small Intestine Terminal Ileumeqtl8.1e-03-0.3019:41608577:T:C
Vaginaeqtl1.2e-02+3.1019:40838571:C:T

FANTOM5 promoters

2 alternative TSS:

Promoter IDTPM avgSamples expressed
1810822.9506226
1810810.209059

Top tissues by expression

showing 100 of 134 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
bloodUBERON:000017895.65gold quality
monocyteCL:000057689.71gold quality
spleenUBERON:000210689.46gold quality
leukocyteCL:000073889.36gold quality
granulocyteCL:000009487.54gold quality
bone marrowUBERON:000237185.94gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.26silver quality
bone marrow cellCL:000209281.48gold quality
vermiform appendixUBERON:000115481.21gold quality
right lungUBERON:000216780.83gold quality
upper lobe of left lungUBERON:000895273.50gold quality
lymph nodeUBERON:000002967.02gold quality
lungUBERON:000204866.74gold quality
smooth muscle tissueUBERON:000113566.17gold quality
gall bladderUBERON:000211066.02gold quality
right coronary arteryUBERON:000162565.92gold quality
left uterine tubeUBERON:000130365.33gold quality
descending thoracic aortaUBERON:000234564.63gold quality
placentaUBERON:000198763.10gold quality
small intestine Peyer’s patchUBERON:000345462.45gold quality
mucosa of stomachUBERON:000119962.24gold quality
omental fat padUBERON:001041461.84gold quality
small intestineUBERON:000210861.46gold quality
left coronary arteryUBERON:000162661.07gold quality
duodenumUBERON:000211460.83gold quality
esophagus mucosaUBERON:000246960.53gold quality
adipose tissueUBERON:000101360.39gold quality
heart left ventricleUBERON:000208460.35gold quality
tibial nerveUBERON:000132359.78gold quality
body of pancreasUBERON:000115059.30gold quality
subcutaneous adipose tissueUBERON:000219059.01gold quality
apex of heartUBERON:000209858.82gold quality
thoracic aortaUBERON:000151558.61gold quality
right adrenal glandUBERON:000123358.26gold quality
ascending aortaUBERON:000149657.94gold quality
minor salivary glandUBERON:000183057.84gold quality
heartUBERON:000094857.58gold quality
left adrenal gland cortexUBERON:003582557.54gold quality
esophagusUBERON:000104357.41gold quality
right adrenal gland cortexUBERON:003582757.29gold quality
liverUBERON:000210757.12gold quality
prostate glandUBERON:000236757.10gold quality
right lobe of liverUBERON:000111456.68gold quality
left adrenal glandUBERON:000123456.66gold quality
body of stomachUBERON:000116156.59gold quality
saliva-secreting glandUBERON:000104456.58gold quality
urinary bladderUBERON:000125556.37gold quality
intestineUBERON:000016056.29gold quality
transverse colonUBERON:000115755.44gold quality
muscle layer of sigmoid colonUBERON:003580555.39gold quality
colonUBERON:000115555.08gold quality
tibial arteryUBERON:000761054.98gold quality
right atrium auricular regionUBERON:000663154.97gold quality
popliteal arteryUBERON:000225054.95gold quality
adrenal glandUBERON:000236954.92gold quality
fallopian tubeUBERON:000388954.64gold quality
rectumUBERON:000105254.53gold quality
lower esophagus muscularis layerUBERON:003583354.40gold quality
lower esophagusUBERON:001347354.34gold quality
material anatomical entityUBERON:000046554.08gold quality
anatomical systemUBERON:000046754.08gold quality
multicellular organismUBERON:000046854.08gold quality
myometriumUBERON:000129653.34gold quality
stomachUBERON:000094553.29gold quality
esophagogastric junction muscularis propriaUBERON:003584153.28gold quality
vaginaUBERON:000099653.18gold quality
right lobe of thyroid glandUBERON:000111952.13gold quality
gastrocnemiusUBERON:000138852.08gold quality
mucosa of transverse colonUBERON:000499152.01gold quality
endocervixUBERON:000045851.90gold quality
pancreasUBERON:000126451.81gold quality
tonsilUBERON:000237251.63gold quality
C1 segment of cervical spinal cordUBERON:000646951.56gold quality
sural nerveUBERON:001548851.52silver quality
thoracic mammary glandUBERON:000520051.17gold quality
metanephros cortexUBERON:001053350.81gold quality
body of uterusUBERON:000985350.40gold quality
muscle of legUBERON:000138350.39gold quality
ectocervixUBERON:001224949.47gold quality
left lobe of thyroid glandUBERON:000112049.43gold quality
muscle tissueUBERON:000238549.35gold quality
uterine cervixUBERON:000000249.27gold quality
substantia nigraUBERON:000203849.21gold quality
adult mammalian kidneyUBERON:000008249.11gold quality
fundus of stomachUBERON:000116048.61gold quality
right ovaryUBERON:000211848.12gold quality
calcaneal tendonUBERON:000370148.10silver quality
skin of legUBERON:000151148.09gold quality
lower esophagus mucosaUBERON:003583447.92gold quality
thyroid glandUBERON:000204647.83gold quality
zone of skinUBERON:000001446.67gold quality
olfactory segment of nasal mucosaUBERON:000538646.58gold quality
hindlimb stylopod muscleUBERON:000425246.00gold quality
cortex of kidneyUBERON:000122545.61gold quality
kidneyUBERON:000211345.13gold quality
skin of abdomenUBERON:000141645.08gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099144.76silver quality
Ammon’s hornUBERON:000195443.84gold quality
pituitary glandUBERON:000000743.57gold quality
amygdalaUBERON:000187643.17gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.34

HPA expression

RNA tissue specificity: Tissue enriched

48 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPM
Bone marrowtissue7.1
Pancreastissue2.0
Spleentissue1.7
Appendixtissue1.7
Vaginatissue0.6
Choroid plexustissue0.6
Medulla oblongatatissue0.6
Lymph nodetissue0.5
Lungtissue0.5
Livertissue0.5
Gallbladdertissue0.5
Urinary bladdertissue0.4
Amygdalatissue0.4
Duodenumtissue0.4
Pituitary glandtissue0.3
Stomach 1tissue0.3
Cerebral cortextissue0.3
Ponstissue0.3
Adipose tissuetissue0.3
Basal gangliatissue0.3
Midbraintissue0.3
Thalamustissue0.3
Hypothalamustissue0.3
Substantia nigratissue0.3
Spinal cordtissue0.3
Endometrium 1tissue0.2
Putamentissue0.2
Placentatissue0.2
Cerebellumtissue0.2
Hippocampustissue0.2
Adrenal glandtissue0.2
Hippocampal formationtissue0.2
Retrosplenial cortextissue0.2
Occipital cortextissue0.2
Heart muscletissue0.1
Ovarytissue0.1
Esophagustissue0.1
Salivary glandtissue0.1
Rectumtissue0.1
Skeletal muscletissue0.1
Smooth muscletissue0.1
Colontissue0.1
Small intestinetissue0.1
Locus coeruleustissue0.1
Prostatetissue0.1
Thymustissue0.1
Tonsiltissue0.1
Postcentral gyrustissue0.1

Brain sub-regions (HPA Brain Atlas): detected in 164; highest nTPM — Blood vessel (1.4), Nucleus raphe pallidus (0.6), Area postrema (0.4), Corticomedial amygdala (0.4), Medial olivary nucleus (0.4).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CEACAM4 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

6 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-488-5P99.2868.12821
HSA-MIR-429199.2068.882969
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-510099.1167.521098
HSA-MIR-6852-3P98.5467.601468
HSA-MIR-446898.0166.851187

Functional genomics

gnomAD constraint: pLI 2.75e-10, LOEUF 1.45, missense Z -0.485 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000221954 — one region, missense o/e 1.07.

Literature-anchored findings (GeneRIF, showing 2)

  • CEACAM4 is expressed in tumor-derived cell lines, and this expression is specific to an medullary thyroid carcinoma derived cell line. (PMID:25152032)
  • CEACAM4 has phagocytic function. (PMID:25567962)

Cross-species orthologs

0 orthologs

Paralogs (24): CEACAM21 (ENSG00000007129), CEACAM7 (ENSG00000007306), CEACAM1 (ENSG00000079385), CEACAM6 (ENSG00000086548), 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), CEACAM20 (ENSG00000273777)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Rattus norvegicusD3ZQE197.4%Diamond
Mus musculusE9QA2897.4%Diamond

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
CEACAM7protein-coding1087
CEACAM21protein-coding90273
LINC01480ncRNA101927931
CEACAM5protein-coding1048

Protein

Protein identifiers

Cell adhesion molecule CEACAM4 — O75871 (reviewed: O75871)

Alternative names: Carcinoembryonic antigen CGM7, Carcinoembryonic antigen-related cell adhesion molecule 4, Non-specific cross-reacting antigen W236

All UniProt accessions (3): A0A077JJN3, O75871, M0R363

UniProt curated annotations — full annotation on UniProt →

Function. Granulocyte orphan receptor that acts as an trigger efficient phagocytosis of attached particles.

Subunit / interactions. Interacts through its phosphorylated ITAM domain with the SH2 domain-containing cytoplasmic proteins involved in signaling processes during phagocytosis.

Subcellular location. Membrane.

Tissue specificity. Granulocytes.

Post-translational modifications. N-glycosylated. The cytoplasmic ITAM-like sequence becomes tyrosine phosphorylated by SRC family PTKs upon ligand-mediated receptor clustering and allows to initiate phagocytosis of bound ligand.

Miscellaneous. To study the function of the orphan receptor CEACAM4 chimeric proteins containing the extracellular bacteria-binding domain of CEACAM3 and the transmembrane and cytoplasmic part of CEACAM4 has been used.

Similarity. Belongs to the immunoglobulin superfamily. CEA family.

RefSeq proteins (4): NP_001349421, NP_001349422, NP_001349424, NP_001808* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007110Ig-like_domDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050831CEA_cell_adhesionFamily

Pfam: PF07686

UniProt features (18 total): glycosylation site 4, sequence variant 2, mutagenesis site 2, sequence conflict 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, region of interest 1, short sequence motif 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75871-F176.990.51

Human Protein Atlas

Protein class: Predicted membrane proteins

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.

Glycosylation sites (4)

TypePositions
N-linked (glcnac…) asparagine111, 126, 57, 104

Mutagenesis-validated functional residues (2)

PositionPhenotype
222no internalization of bacteria; when associated with f-233.
233no internalization of bacteria; when associated with f-222.

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: 63 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, TSENG_IRS1_TARGETS_UP, MODULE_45, MODULE_64, GOCC_CELL_SURFACE, GOBP_VESICLE_MEDIATED_TRANSPORT, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, CAR_MYST2, MODULE_157, CAR_MLANA, SANSOM_APC_TARGETS_DN, AFFAR_YY1_TARGETS_DN, MODULE_242, GOBP_IMPORT_INTO_CELL, MODULE_20

GO Biological Process (3): regulation of immune system process (GO:0002682), phagocytosis (GO:0006909), signal transduction (GO:0007165)

GO Molecular Function (2): protein tyrosine kinase binding (GO:1990782), protein binding (GO:0005515)

GO Cellular Component (3): plasma membrane (GO:0005886), cell surface (GO:0009986), membrane (GO:0016020)

GO top-level categories

13 GO namespaces:

CategoryTerms
cellular anatomical structure2
immune system process1
regulation of biological process1
endocytosis1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
protein kinase binding1
binding1
membrane1
cell periphery1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 8 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO termNSEvidence
phagocytosisBPdirect assay

Protein interactions and networks

STRING

showing 15 of 720 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
CEACAM4CEACAM20Q6UY09610
CEACAM4GK5Q6ZS86547
CEACAM4CYP2A13Q16696544
CEACAM4UNC79Q9P2D8536
CEACAM4CYP2A7P20853513
CEACAM4NALCNQ8IZF0500
CEACAM4UNC80Q8N2C7497
CEACAM4A0A096LNM5A0A096LNM5490
CEACAM4PLA2G7Q13093487
CEACAM4SLC12A3P55017444
CEACAM4CYP2A6P00190440
CEACAM4IGDCC3Q8IVU1400
CEACAM4ADGRE5P48960370
CEACAM4CD177Q8N6Q3367
CEACAM4IGSF23A1L1A6365

IntAct

Human interaction partners of CEACAM4 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

PartnerInteraction typeMIscoreRecords
FLT4physical association0.4002
PDCD1LG2physical association0.4001

Disease & clinical

Genetic variants

Variant evidence for CEACAM4: 47 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign3
Benign0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 37 predictions of 634):

Position(s)EffectΔscoreSites
19:41621653donor_gain0.9900
19:41626898–41626899donor_loss0.99005
19:41619396–41619397acceptor_loss0.98006
19:41620573–41620574donor_loss0.98005
19:41620628–41620629acceptor_loss0.98006
19:41620650acceptor_gain0.9800
19:41619712–41619713acceptor_loss0.97006
19:41619668–41619669donor_loss0.96005
19:41619718acceptor_gain0.9600
19:41619945donor_gain0.9600

AlphaMissense

180 missense substitutions predicted likely pathogenic (of 1,548 scored), across 76 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
D11680.8060.896
W6770.9390.984
G7060.7770.893
E9960.7410.912
Y12050.9170.963
G9250.8630.870
F10950.7430.914
G10540.9170.965
G11840.7800.828
S10640.7790.975
N10440.7540.815
Y6540.7500.922
G15940.7420.801
H6840.7220.881
S9640.6900.697
G4840.6850.833
F3640.6590.661
L10730.9030.960
L12230.8820.954
L5330.8660.918

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:619159 | disease phenotypes:

GWAS associations

2 associations:

StudyTraitp-value
GCST004744_57Lung adenocarcinoma3e-7
GCST007160_30Refractive astigmatism8e-6

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

ChemicalActions (top 5)PubMed papers
triphenyl phosphateaffects expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
theaflavin-3,3’-digallateaffects expression1
Acetaminophendecreases expression1
Aldehydesincreases expression1
Atrazineincreases expression1
Benzo(a)pyreneincreases methylation1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Tretinoinincreases expression1
Aflatoxin B1increases methylation1

Clinical trials (associated diseases)

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

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