CERCAM

Summary

CERCAM (cerebral endothelial cell adhesion molecule, HGNC:23723) is a protein-coding gene on chromosome 9q34.11, encoding Inactive glycosyltransferase 25 family member 3 (Q5T4B2). Probable cell adhesion protein involved in leukocyte transmigration across the blood-brain barrier.

Enables identical protein binding activity. Acts upstream of or within cell adhesion. Predicted to be located in plasma membrane.

Source: NCBI Gene 51148 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 143 total — 2 pathogenic
• MANE Select transcript: NM_016174

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23723
Approved symbol	CERCAM
Name	cerebral endothelial cell adhesion molecule
Location	9q34.11
Locus type	gene with protein product
Status	Approved
Aliases	GLT25D3
Ensembl gene	ENSG00000167123
Ensembl biotype	protein_coding
OMIM	616626
Entrez	51148

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 17 protein_coding, 4 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000372838, ENST00000372842, ENST00000411852, ENST00000420034, ENST00000420512, ENST00000447915, ENST00000463535, ENST00000472858, ENST00000483737, ENST00000483893, ENST00000487001, ENST00000493788, ENST00000895870, ENST00000895871, ENST00000895872, ENST00000895873, ENST00000951767, ENST00000951768, ENST00000951769, ENST00000951770, ENST00000951771, ENST00000951772, ENST00000951773

RefSeq mRNA: 2 — MANE Select: NM_016174 NM_001286760, NM_016174

CCDS: CCDS6901, CCDS69675

Canonical transcript exons

ENST00000372838 — 13 exons

Exon	Start	End
ENSE00001109960	128434410	128434613
ENSE00001218481	128436849	128437347
ENSE00001720937	128420857	128421074
ENSE00001785614	128424138	128424272
ENSE00003525804	128428302	128428421
ENSE00003534701	128431171	128431303
ENSE00003591901	128422868	128422978
ENSE00003605963	128428930	128429036
ENSE00003612922	128434102	128434229
ENSE00003626739	128424410	128424614
ENSE00003660314	128428757	128428833
ENSE00003788370	128435653	128435905
ENSE00003790268	128423146	128423263

Expression profiles

Bgee: expression breadth ubiquitous, 209 present calls, max score 99.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 70.0487 / max 993.3746, expressed in 1707 samples.

FANTOM5 promoters (18 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98776	61.0149	1700
98766	1.8305	88
98775	1.2942	806
98769	1.0429	72
98768	0.7964	76
98778	0.7471	432
98767	0.7373	80
98777	0.4896	264
98780	0.4372	266
98770	0.2517	65

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	99.35	gold quality
spinal cord	UBERON:0002240	99.20	gold quality
inferior vagus X ganglion	UBERON:0005363	99.17	gold quality
lateral globus pallidus	UBERON:0002476	99.09	gold quality
putamen	UBERON:0001874	98.88	gold quality
medulla oblongata	UBERON:0001896	98.77	gold quality
superior vestibular nucleus	UBERON:0007227	98.63	gold quality
ventral tegmental area	UBERON:0002691	98.46	gold quality
stromal cell of endometrium	CL:0002255	98.37	gold quality
subthalamic nucleus	UBERON:0001906	98.23	gold quality
midbrain	UBERON:0001891	98.16	gold quality
substantia nigra	UBERON:0002038	98.12	gold quality
amygdala	UBERON:0001876	98.05	gold quality
dorsal plus ventral thalamus	UBERON:0001897	97.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.87	gold quality
caudate nucleus	UBERON:0001873	97.55	gold quality
substantia nigra pars reticulata	UBERON:0001966	97.43	gold quality
hypothalamus	UBERON:0001898	97.32	gold quality
right frontal lobe	UBERON:0002810	97.18	gold quality
nucleus accumbens	UBERON:0001882	96.81	gold quality
corpus callosum	UBERON:0002336	96.72	gold quality
adenohypophysis	UBERON:0002196	96.08	gold quality
Ammon’s horn	UBERON:0001954	95.89	gold quality
pituitary gland	UBERON:0000007	95.79	gold quality
substantia nigra pars compacta	UBERON:0001965	95.62	gold quality
pons	UBERON:0000988	94.98	gold quality
anterior cingulate cortex	UBERON:0009835	94.78	gold quality
right coronary artery	UBERON:0001625	94.62	gold quality
ascending aorta	UBERON:0001496	94.35	gold quality
thoracic aorta	UBERON:0001515	94.32	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-30	yes	1381.85
E-HCAD-25	yes	49.68
E-CURD-112	yes	15.53
E-HCAD-13	yes	12.72
E-ANND-3	yes	11.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting CERCAM, 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-4713-3P	100.00	65.92	505
HSA-MIR-4500	99.99	72.72	2367
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-4728-5P	99.85	69.39	4718

Literature-anchored findings (GeneRIF, showing 1)

• The oncogenic role of the cerebral endothelial cell adhesion molecule (CERCAM) in bladder cancer cells in vitro and in vivo. (PMID:34105305)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	cercam	ENSDARG00000079049
mus_musculus	Cercam	ENSMUSG00000039787
rattus_norvegicus	Cercam	ENSRNOG00000026604
drosophila_melanogaster	CG31915	FBGN0051915
caenorhabditis_elegans		WBGENE00008426

Paralogs (5): PLOD1 (ENSG00000083444), PLOD3 (ENSG00000106397), COLGALT1 (ENSG00000130309), PLOD2 (ENSG00000152952), COLGALT2 (ENSG00000198756)

Protein

Protein identifiers

Inactive glycosyltransferase 25 family member 3 — Q5T4B2 (reviewed: Q5T4B2)

Alternative names: Cerebral endothelial cell adhesion molecule

All UniProt accessions (5): B7ZBS8, B7ZBS9, B7ZBT0, Q5T4B2, X6RL83

UniProt curated annotations — full annotation on UniProt →

Function. Probable cell adhesion protein involved in leukocyte transmigration across the blood-brain barrier. Does not express any beta-galactosyltransferase activity in vitro.

Subcellular location. Endoplasmic reticulum lumen.

Tissue specificity. Ubiquitous. Highly expressed in secretory and nervous tissues.

Similarity. Belongs to the glycosyltransferase 25 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5T4B2-1	1	yes
Q5T4B2-2	2

RefSeq proteins (2): NP_001273689, NP_057258* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002654	Glyco_trans_25	Domain
IPR029044	Nucleotide-diphossugar_trans	Homologous_superfamily
IPR050757	Collagen_mod_GT25	Family

Pfam: PF01755

UniProt features (17 total): mutagenesis site 5, glycosylation site 4, sequence conflict 2, signal peptide 1, chain 1, region of interest 1, short sequence motif 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T4B2-F1	89.17	0.78

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): 75, 153, 237, 360

Mutagenesis-validated functional residues (5):

Position	Phenotype
440	no effect on lack of galactosyltransferase activity in a chimeric construct with colgalt1. exhibits some galactosyltrans
450	exhibits some galactosyltransferase activity; when associated with d-440; m-451; q-452 and v-453 in a chimeric construct
451	exhibits some galactosyltransferase activity; when associated with d-440; r-450; q-452 and v-453 in a chimeric construct
452	exhibits some galactosyltransferase activity; when associated with d-440; r-450; m-451 and v-453 in a chimeric construct
453	exhibits some galactosyltransferase activity; when associated with d-440; r-450; m-451 and q-452 in a chimeric construct

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 120 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GGGTGGRR_PAX4_03, GOBP_CELL_CELL_ADHESION, ZIC1_01, GOBP_LEUKOCYTE_CELL_CELL_ADHESION, DOUGLAS_BMI1_TARGETS_UP, CTGYNNCTYTAA_UNKNOWN, AP2_Q6_01, AP2GAMMA_01, GOCC_ENDOPLASMIC_RETICULUM_LUMEN, GOMF_HEXOSYLTRANSFERASE_ACTIVITY, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, GOMF_GALACTOSYLTRANSFERASE_ACTIVITY, GOMF_UDP_GLYCOSYLTRANSFERASE_ACTIVITY, AP2ALPHA_01

GO Biological Process (2): cell adhesion (GO:0007155), leukocyte cell-cell adhesion (GO:0007159)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (3): endoplasmic reticulum lumen (GO:0005788), plasma membrane (GO:0005886), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	1
cell-cell adhesion	1
protein binding	1
binding	1
endoplasmic reticulum	1
intracellular organelle lumen	1
membrane	1
cell periphery	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

504 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CERCAM	LYPLA2	O95372	453
CERCAM	LHPP	Q9H008	445
CERCAM	AHNAK	Q09666	396
CERCAM	STOX2	Q9P2F5	389
CERCAM	TMEM217	Q8N7C4	387
CERCAM	TMEM217B	A0A494BZU4	387
CERCAM	NF2	P35240	369
CERCAM	NRN1L	Q496H8	351
CERCAM	ERICH5	Q6P6B1	348
CERCAM	ZFP14	Q9HCL3	331
CERCAM	TMEM35A	Q53FP2	328
CERCAM	SPDYE1	Q8NFV5	326
CERCAM	FAM228B	P0C875	326
CERCAM	MANBAL	Q9NQG1	322
CERCAM	CCDC86	Q9H6F5	320
CERCAM	LRRC57	Q8N9N7	320

IntAct

188 interactions, top by confidence:

A	B	Type	Score
C1QTNF9	C1QTNF9B	psi-mi:“MI:0914”(association)	0.780
CA10	WDHD1	psi-mi:“MI:0914”(association)	0.640
CERCAM	ABHD5	psi-mi:“MI:0915”(physical association)	0.560
GEMIN4	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.560
KLHL38	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
LASP1	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
SOHLH1	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	FNDC11	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	FANCL	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	KRTAP3-3	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	UBL5	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	P4HA3	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	TENT5B	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	MAGED1	psi-mi:“MI:0915”(physical association)	0.560
POGZ	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
POU4F2	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	KRTAP26-1	psi-mi:“MI:0915”(physical association)	0.560
OTX1	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	ATG9A	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-2	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
KRTAP15-1	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
VENTX	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
HOXA1	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CREB5	CERCAM	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	KRTAP8-1	psi-mi:“MI:0915”(physical association)	0.560
CERCAM	RHOXF2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (146): GOPC (Two-hybrid), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS), CERCAM (Affinity Capture-MS)

ESM2 similar proteins: A0JPH3, A1YGR5, A3KGW5, A5PMF6, A7MB73, O00469, O14638, O43909, O77588, P06802, P15396, P24802, P26572, P27115, P27808, P50127, P79948, P79949, P97675, Q02809, Q09325, Q32NJ7, Q3L7M0, Q5IGR6, Q5R5M5, Q5R9N3, Q5T4B2, Q5U309, Q5U483, Q5XPT3, Q5ZLK4, Q63321, Q66PG1, Q66PG2, Q66PG4, Q6DYE8, Q6NVG7, Q6P7A1, Q6P9A2, Q6PA90

Diamond homologs: A0JPH3, A3KGW5, A5PK45, A5PMF6, A7MB73, O77588, Q17FB8, Q29NU5, Q5T4B2, Q5U309, Q5U367, Q5U483, Q6NVG7, Q7Q021, Q811A3, Q8IPK4, Q8IYK4, Q8K297, Q8NBJ5, Q9R0E1, Q9R0E2, P57033, P71398, Q50947, Q50950, Q51116, Q51117, Q57394, Q5UQ62, Q5UQC3, Q02809, Q5R9N3, Q9VTH0, Q03974, Q63321, Q05770, Q57125, O60568, Q5R6K5, O00469

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	118
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
815297	GRCh37/hg19 9q34.11(chr9:130957344-132310210)x1	Pathogenic
984763	GRCh37/hg19 9q34.11(chr9:130412438-131423964)x1	Pathogenic

SpliceAI

2240 predictions. Top by Δscore:

Variant	Effect	Δscore
9:128422866:A:AG	acceptor_gain	1.0000
9:128422866:AGGTG:A	acceptor_loss	1.0000
9:128422867:G:GG	acceptor_gain	1.0000
9:128422867:G:GT	acceptor_loss	1.0000
9:128422867:GGTGT:G	acceptor_gain	1.0000
9:128422958:G:GT	donor_gain	1.0000
9:128422968:G:GT	donor_gain	1.0000
9:128423219:G:GT	donor_gain	1.0000
9:128423239:G:GT	donor_gain	1.0000
9:128423240:A:T	donor_gain	1.0000
9:128423262:TGGTG:T	donor_loss	1.0000
9:128423264:G:A	donor_loss	1.0000
9:128423265:T:A	donor_loss	1.0000
9:128423269:G:GT	donor_gain	1.0000
9:128424407:CA:C	acceptor_loss	1.0000
9:128424408:A:AG	acceptor_gain	1.0000
9:128424408:A:T	acceptor_loss	1.0000
9:128424408:AG:A	acceptor_gain	1.0000
9:128424408:AGG:A	acceptor_gain	1.0000
9:128424409:G:GA	acceptor_gain	1.0000
9:128424409:GG:G	acceptor_gain	1.0000
9:128424409:GGG:G	acceptor_gain	1.0000
9:128424409:GGGCT:G	acceptor_gain	1.0000
9:128424611:GCTG:G	donor_gain	1.0000
9:128424612:CTGGT:C	donor_loss	1.0000
9:128424613:TGGTG:T	donor_loss	1.0000
9:128424615:G:GG	donor_gain	1.0000
9:128424616:T:A	donor_loss	1.0000
9:128428418:CTAG:C	donor_loss	1.0000
9:128428420:AGGT:A	donor_loss	1.0000

AlphaMissense

3873 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:128424248:C:A	N179K	0.998
9:128424248:C:G	N179K	0.998
9:128428337:G:T	G268W	0.997
9:128428338:G:A	G268E	0.997
9:128424249:T:C	F180L	0.996
9:128424251:C:A	F180L	0.996
9:128424251:C:G	F180L	0.996
9:128424252:T:A	W181R	0.996
9:128424252:T:C	W181R	0.996
9:128424244:C:T	S178F	0.995
9:128424434:T:C	Y196H	0.995
9:128422917:T:A	W83R	0.994
9:128422917:T:C	W83R	0.994
9:128424254:G:C	W181C	0.994
9:128424254:G:T	W181C	0.994
9:128424486:T:A	V213D	0.994
9:128424477:T:A	V210D	0.993
9:128428324:T:A	N263K	0.993
9:128428324:T:G	N263K	0.993
9:128428338:G:T	G268V	0.993
9:128424214:C:A	A168D	0.992
9:128424250:T:C	F180S	0.992
9:128428337:G:A	G268R	0.992
9:128428337:G:C	G268R	0.992
9:128423215:G:C	K126N	0.991
9:128423215:G:T	K126N	0.991
9:128424243:T:C	S178P	0.991
9:128424244:C:A	S178Y	0.991
9:128424435:A:G	Y196C	0.991
9:128424448:G:C	K200N	0.991

dbSNP variants (sampled 300 via entrez): RS1000025818 (9:128432507 C>G), RS1000116297 (9:128436015 C>T), RS1000304861 (9:128436933 C>G), RS1000335034 (9:128420706 G>A,C), RS1000433108 (9:128430932 C>T), RS1000454858 (9:128434808 C>G,T), RS1001046655 (9:128420334 G>T), RS1001048968 (9:128427511 C>T), RS1001112394 (9:128427203 C>T), RS1001226267 (9:128432859 G>A), RS1001279481 (9:128421867 T>G), RS1001445915 (9:128430817 A>C,G), RS1001497286 (9:128419818 G>A), RS1001699832 (9:128417687 G>T), RS1001730853 (9:128417365 G>T)

Disease associations

OMIM: gene MIM:616626 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): infantile epilepsy syndrome (MONDO:0020071)

Orphanet (1): OBSOLETE: Infantile epilepsy syndrome (Orphanet:98258)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003252_2	Systemic lupus erythematosus	2.000000e-06
GCST005951_65	Body mass index	5.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	3
aristolochic acid I	decreases expression	1
bisphenol F	increases expression	1
2,4,6-tribromophenol	decreases expression	1
triphenyl phosphate	affects expression	1
deoxynivalenol	decreases expression	1
decabromobiphenyl ether	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
bisphenol S	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases expression	1
Carbamazepine	affects expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Nickel	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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