CEACAM21

Summary

CEACAM21 (CEA cell adhesion molecule 21, HGNC:28834) is a protein-coding gene on chromosome 19q13.2, encoding Cell adhesion molecule CEACAM21 (Q3KPI0).

Predicted to be involved in T cell activation and immune response. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane.

Source: NCBI Gene 90273 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 63 total
• MANE Select transcript: NM_001098506

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28834
Approved symbol	CEACAM21
Name	CEA cell adhesion molecule 21
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	R29124_1, FLJ13540
Ensembl gene	ENSG00000007129
Ensembl biotype	protein_coding
OMIM	618191
Entrez	90273

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000187608, ENST00000401445, ENST00000407170, ENST00000457737, ENST00000482870, ENST00000618577, ENST00000632983, ENST00000890424, ENST00000890425, ENST00000967641

RefSeq mRNA: 4 — MANE Select: NM_001098506 NM_001098506, NM_001288773, NM_001290113, NM_033543

CCDS: CCDS46086, CCDS46087, CCDS74373

Canonical transcript exons

ENST00000401445 — 7 exons

Exon	Start	End
ENSE00001476587	41584347	41584443
ENSE00001813751	41586464	41586844
ENSE00001821184	41576166	41576338
ENSE00003506004	41579353	41579628
ENSE00003558986	41585443	41585495
ENSE00003587232	41577200	41577559
ENSE00003603125	41585840	41585871

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 92.02.

FANTOM5 (CAGE): breadth broad, TPM avg 7.9132 / max 396.1095, expressed in 580 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176040	6.8625	414
176044	0.7843	290
208829	0.1197	49
176042	0.1143	25
176043	0.0324	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lymph node	UBERON:0000029	92.02	gold quality
granulocyte	CL:0000094	91.88	gold quality
blood	UBERON:0000178	90.93	gold quality
bone marrow cell	CL:0002092	88.57	gold quality
bone marrow	UBERON:0002371	88.50	gold quality
spleen	UBERON:0002106	87.14	gold quality
vermiform appendix	UBERON:0001154	85.65	gold quality
placenta	UBERON:0001987	79.09	gold quality
leukocyte	CL:0000738	78.71	gold quality
monocyte	CL:0000576	77.66	gold quality
hypothalamus	UBERON:0001898	77.44	gold quality
gall bladder	UBERON:0002110	76.86	gold quality
right lung	UBERON:0002167	76.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.62	silver quality
small intestine Peyer’s patch	UBERON:0003454	75.46	gold quality
rectum	UBERON:0001052	75.18	gold quality
substantia nigra	UBERON:0002038	74.86	gold quality
small intestine	UBERON:0002108	74.23	gold quality
upper lobe of left lung	UBERON:0008952	73.55	gold quality
duodenum	UBERON:0002114	72.53	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.22	gold quality
lung	UBERON:0002048	71.75	gold quality
omental fat pad	UBERON:0010414	69.68	gold quality
smooth muscle tissue	UBERON:0001135	69.57	gold quality
apex of heart	UBERON:0002098	69.38	gold quality
right coronary artery	UBERON:0001625	69.23	gold quality
tonsil	UBERON:0002372	68.99	gold quality
mucosa of transverse colon	UBERON:0004991	68.43	gold quality
adipose tissue	UBERON:0001013	68.07	gold quality
subcutaneous adipose tissue	UBERON:0002190	66.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-5	yes	155.99
E-ANND-3	no	1.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting CEACAM21, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-5100	99.11	67.52	1098
HSA-MIR-599	98.32	66.99	1037
HSA-MIR-592	96.59	67.59	817

Literature-anchored findings (GeneRIF, showing 1)

• This study revealed CEACAM21 as novel schizophrenia candidate genes in the Jewish population (PMID:21682944)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ceacam9	ENSMUSG00000007209
mus_musculus	Ceacam15	ENSMUSG00000078795
rattus_norvegicus	Ceacam15	ENSRNOG00000028617
rattus_norvegicus	Ceacam9	ENSRNOG00000046915
rattus_norvegicus	Ceacam15l1	ENSRNOG00000065825

Paralogs (24): 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), CEACAM20 (ENSG00000273777)

Protein

Protein identifiers

Cell adhesion molecule CEACAM21 — Q3KPI0 (reviewed: Q3KPI0)

Alternative names: Carcinoembryonic antigen-related cell adhesion molecule 21

All UniProt accessions (3): Q3KPI0, A0A0B4J1W4, A0A0J9YX60

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the immunoglobulin superfamily. CEA family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q3KPI0-1	1	yes
Q3KPI0-2	2
Q3KPI0-3	3

RefSeq proteins (4): NP_001091976, NP_001275702, NP_001277042, NP_291021 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013106	Ig_V-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050831	CEA_cell_adhesion	Family

Pfam: PF07686, PF13927

UniProt features (13 total): splice variant 2, sequence variant 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, region of interest 1, glycosylation site 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3KPI0-F1	85.54	0.72

Functional residue map

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

Disulfide bonds (1): 166–214

Glycosylation sites (1): 111

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 124 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, GOCC_CELL_SURFACE, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, BROWN_MYELOID_CELL_DEVELOPMENT_UP, AFFAR_YY1_TARGETS_UP, DOUGLAS_BMI1_TARGETS_UP, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, GOCC_SIDE_OF_MEMBRANE, MATSUDA_NATURAL_KILLER_DIFFERENTIATION, YOSHIMURA_MAPK8_TARGETS_UP, MIKKELSEN_ES_ICP_WITH_H3K4ME3

GO Biological Process (2): immune response (GO:0006955), T cell activation (GO:0042110)

GO Molecular Function (0):

GO Cellular Component (2): external side of plasma membrane (GO:0009897), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
immune system process	1
response to stimulus	1
lymphocyte activation	1
plasma membrane	1
cell surface	1
side of membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1220 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CEACAM21	CEACAM19	Q7Z692	651
CEACAM21	SYK	P43405	558
CEACAM21	VAV1	P15498	490
CEACAM21	CD55	P08174	458
CEACAM21	CD79A	P11912	443
CEACAM21	ERV3-1	Q14264	436
CEACAM21	ERVFRD-1	P60508	427
CEACAM21	ERVW-1	Q9UQF0	422
CEACAM21	DMAC2	Q9NW81	418
CEACAM21	EFHB	Q8N7U6	404
CEACAM21	ESR1	P03372	397
CEACAM21	CD40LG	P29965	387
CEACAM21	HOXA2	O43364	370
CEACAM21	SIGLEC5	O15389	367
CEACAM21	CAPSL	Q8WWF8	336

IntAct

7 interactions, top by confidence:

A	B	Type	Score
DPPA4	ALOX12B	psi-mi:“MI:0914”(association)	0.530
LILRA6	CEACAM21	psi-mi:“MI:0915”(physical association)	0.400
LILRB1	CEACAM21	psi-mi:“MI:0915”(physical association)	0.400
CEACAM21	MET	psi-mi:“MI:0914”(association)	0.350
CEACAM21	GAPDHS	psi-mi:“MI:0914”(association)	0.350
CEACAM21	VGLL4	psi-mi:“MI:0914”(association)	0.350

BioGRID (148): KIAA0319L (Affinity Capture-MS), HLA-F (Affinity Capture-MS), ABHD14A (Affinity Capture-MS), KIDINS220 (Affinity Capture-MS), FAT4 (Affinity Capture-MS), ATP6V0A1 (Affinity Capture-MS), ABCB6 (Affinity Capture-MS), ATR (Affinity Capture-MS), PTK7 (Affinity Capture-MS), NCR3LG1 (Affinity Capture-MS), PCDHGA11 (Affinity Capture-MS), PCDHGC3 (Affinity Capture-MS), KIAA1524 (Affinity Capture-MS), PCDH20 (Affinity Capture-MS), XPR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0E4BZH1, A4QPC6, A5D7V5, A7TZE6, A7TZF0, A7TZF3, A7XUX6, A7XV04, A7XV07, A8K4G0, A8MVZ5, O70355, P08508, P18892, P24071, P31994, P55803, P78410, P79391, Q13410, Q16653, Q29ZQ1, Q3KPI0, Q58DF9, Q5R7W8, Q5R960, Q5R996, Q61885, Q62556, Q63345, Q6Q8B3, Q6UXZ3, Q6XJV4, Q6XJV6, Q7KYR7, Q7TST0, Q7YR73, Q8BTP3, Q8K249, Q8TD46

Diamond homologs: A0A0B4J1L0, D3ZQE1, E9QA28, O75871, P06731, P11464, P11465, P13688, P16573, P31809, P31997, P40198, P40199, Q00887, Q00888, Q00889, Q13046, Q14002, Q15238, Q16557, Q2WEN9, Q3KPI0, Q3UKK2, Q61400, Q63111, Q810J1, Q925P2, Q9D2Z1, Q9UQ72, Q9UQ74, A4FUY1, A6QQC6, A8MVW5, D3YXG0, D3ZB51, E9PZ19, O08775, P13595, P13596, P35968

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1055 predictions. Top by Δscore:

Variant	Effect	Δscore
19:41579627:AT:A	donor_gain	1.0000
19:41579627:ATG:A	donor_loss	1.0000
19:41579628:TG:T	donor_loss	1.0000
19:41579629:G:GG	donor_gain	1.0000
19:41579629:GTGA:G	donor_loss	1.0000
19:41579630:T:G	donor_loss	1.0000
19:41579631:GAGT:G	donor_loss	1.0000
19:41576335:ACAGG:A	donor_loss	0.9900
19:41576336:CAGG:C	donor_loss	0.9900
19:41576337:AGGTG:A	donor_loss	0.9900
19:41576339:G:GA	donor_loss	0.9900
19:41577198:A:AG	acceptor_gain	0.9900
19:41577199:G:GG	acceptor_gain	0.9900
19:41577199:GCCTC:G	acceptor_gain	0.9900
19:41577558:CGGTG:C	donor_loss	0.9900
19:41577559:GGT:G	donor_loss	0.9900
19:41577560:GTGA:G	donor_loss	0.9900
19:41579625:AAAT:A	donor_gain	0.9900
19:41579626:AAT:A	donor_gain	0.9900
19:41584345:A:AG	acceptor_gain	0.9900
19:41584346:G:GA	acceptor_gain	0.9900
19:41584346:GC:G	acceptor_gain	0.9900
19:41584346:GCA:G	acceptor_gain	0.9900
19:41584441:CAGGT:C	donor_loss	0.9900
19:41584442:AGG:A	donor_loss	0.9900
19:41584443:GG:G	donor_loss	0.9900
19:41584444:GT:G	donor_loss	0.9900
19:41584445:T:G	donor_loss	0.9900
19:41585496:G:T	donor_loss	0.9900
19:41585497:T:A	donor_loss	0.9900

AlphaMissense

1899 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:41579459:G:C	W177C	0.992
19:41579459:G:T	W177C	0.992
19:41579457:T:A	W177R	0.991
19:41579457:T:C	W177R	0.991
19:41577336:G:C	W67C	0.987
19:41577336:G:T	W67C	0.987
19:41577334:T:A	W67R	0.982
19:41577334:T:C	W67R	0.982
19:41579563:A:G	Y212C	0.982
19:41579562:T:G	Y212D	0.981
19:41579568:T:A	C214S	0.981
19:41579569:G:C	C214S	0.981
19:41579562:T:C	Y212H	0.978
19:41579563:A:C	Y212S	0.977
19:41579601:A:C	S225R	0.972
19:41579603:C:A	S225R	0.972
19:41579603:C:G	S225R	0.972
19:41579458:G:C	W177S	0.969
19:41579424:T:A	C166S	0.968
19:41579425:G:C	C166S	0.968
19:41579424:T:C	C166R	0.965
19:41579419:T:C	L164P	0.964
19:41577428:G:C	R98P	0.963
19:41577455:T:C	L107P	0.959
19:41577493:T:G	Y120D	0.956
19:41579568:T:C	C214R	0.955
19:41577482:A:T	D116V	0.954
19:41577482:A:C	D116A	0.953
19:41577500:T:C	L122P	0.953
19:41579566:A:C	Q213P	0.953

dbSNP variants (sampled 300 via entrez): RS1000057280 (19:41575631 T>C), RS1000141865 (19:41584189 C>T), RS1000427941 (19:41551959 C>T), RS1000534793 (19:41575294 G>A), RS1000546555 (19:41550562 G>A), RS1000597904 (19:41556816 G>T), RS1000611675 (19:41551771 A>G), RS1000745915 (19:41585275 G>A), RS1000812150 (19:41586565 C>A,T), RS1000841246 (19:41569548 G>A), RS1000955451 (19:41569327 C>T), RS1001203955 (19:41552875 C>T), RS1001261990 (19:41560205 A>G), RS1001407522 (19:41563658 G>A), RS1001783423 (19:41565885 C>T)

Disease associations

OMIM: gene MIM:618191 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001119_2	Schizophrenia	1.000000e-07
GCST001714_1	Prostate cancer	1.000000e-08
GCST001714_2	Prostate cancer	2.000000e-12
GCST004744_58	Lung adenocarcinoma	3.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	increases activity, affects binding, decreases expression	1
arsenite	affects expression	1
perfluorooctanoic acid	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
Amphotericin B	increases expression	1
Benzo(a)pyrene	affects methylation	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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