SMAGP

Summary

SMAGP (small cell adhesion glycoprotein, HGNC:26918) is a protein-coding gene on chromosome 12q13.13, encoding Small cell adhesion glycoprotein (Q0VAQ4). May play a role in epithelial cell-cell contacts.

Located in cell junction; nucleoplasm; and plasma membrane.

Source: NCBI Gene 57228 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_001031628

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26918
Approved symbol	SMAGP
Name	small cell adhesion glycoprotein
Location	12q13.13
Locus type	gene with protein product
Status	Approved
Aliases	MGC149453, MGC149454, hSMAGP
Ensembl gene	ENSG00000170545
Ensembl biotype	protein_coding
OMIM	621255
Entrez	57228

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 nonsense_mediated_decay

ENST00000380103, ENST00000398453, ENST00000603798, ENST00000603838, ENST00000603864, ENST00000604188, ENST00000605426, ENST00000605627, ENST00000889732, ENST00000949616

RefSeq mRNA: 2 — MANE Select: NM_001031628 NM_001031628, NM_001033873

CCDS: CCDS44889

Canonical transcript exons

ENST00000603798 — 4 exons

Exon	Start	End
ENSE00001483732	51270256	51270415
ENSE00003497111	51244558	51246119
ENSE00003528612	51269245	51269316
ENSE00003578324	51246751	51246831

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 98.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.3694 / max 224.5595, expressed in 1668 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
130949	10.1329	1593
130946	2.9941	592
130948	2.9921	1106
130945	2.0530	958
130944	0.8664	498
130947	0.2267	135
130943	0.1042	44

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	98.10	gold quality
mucosa of transverse colon	UBERON:0004991	97.08	gold quality
esophagus mucosa	UBERON:0002469	97.02	gold quality
tongue squamous epithelium	UBERON:0006919	96.82	gold quality
pharyngeal mucosa	UBERON:0000355	95.87	gold quality
rectum	UBERON:0001052	95.67	gold quality
esophagus squamous epithelium	UBERON:0006920	95.07	gold quality
epithelium of esophagus	UBERON:0001976	94.85	gold quality
placenta	UBERON:0001987	94.55	gold quality
colonic mucosa	UBERON:0000317	93.66	gold quality
nasal cavity epithelium	UBERON:0005384	93.66	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.62	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.46	gold quality
oral cavity	UBERON:0000167	93.15	gold quality
squamous epithelium	UBERON:0006914	92.94	gold quality
ileal mucosa	UBERON:0000331	92.45	gold quality
cervix epithelium	UBERON:0004801	91.77	gold quality
palpebral conjunctiva	UBERON:0001812	91.51	gold quality
transverse colon	UBERON:0001157	91.47	gold quality
vagina	UBERON:0000996	91.38	gold quality
pancreatic ductal cell	CL:0002079	90.98	gold quality
skin of abdomen	UBERON:0001416	90.12	gold quality
skin of leg	UBERON:0001511	89.78	gold quality
amniotic fluid	UBERON:0000173	89.57	gold quality
metanephros cortex	UBERON:0010533	89.36	gold quality
penis	UBERON:0000989	89.31	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.29	gold quality
cervix squamous epithelium	UBERON:0006922	89.23	silver quality
mammalian vulva	UBERON:0000997	88.69	gold quality
gingiva	UBERON:0001828	88.67	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	1291.74
E-MTAB-6911	yes	204.12
E-HCAD-10	yes	31.99
E-MTAB-8271	yes	19.10
E-ANND-3	yes	15.58
E-HCAD-13	yes	7.63

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• SMAGP knockdown inhibits the malignant phenotypes of glioblastoma cells by inactivating the PI3K/Akt pathway. (PMID:33049294)
• SMAGP regulates doxorubicin sensitivity in triple-negative breast cancer cells via modulating mitochondrial respiration. (PMID:36436062)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:113337	ENSDARG00000041998
danio_rerio	si:ch211-222f23.6	ENSDARG00000042880
danio_rerio	zgc:172122	ENSDARG00000079191
danio_rerio	si:ch211-214p13.3	ENSDARG00000087403
danio_rerio	si:ch211-141e20.2	ENSDARG00000093349
danio_rerio	sc:d189	ENSDARG00000102858
mus_musculus	Smagp	ENSMUSG00000053559
rattus_norvegicus	Smagp	ENSRNOG00000062981
drosophila_melanogaster	Fas3	FBGN0000636

Paralogs (14): PVR (ENSG00000073008), CD200 (ENSG00000091972), CADM4 (ENSG00000105767), CRTAM (ENSG00000109943), NECTIN1 (ENSG00000110400), NECTIN2 (ENSG00000130202), NECTIN4 (ENSG00000143217), CD226 (ENSG00000150637), CADM3 (ENSG00000162706), CADM2 (ENSG00000175161), NECTIN3 (ENSG00000177707), TIGIT (ENSG00000181847), CADM1 (ENSG00000182985), NCR3 (ENSG00000204475)

Protein

Protein identifiers

Small cell adhesion glycoprotein — Q0VAQ4 (reviewed: Q0VAQ4)

Alternative names: Small transmembrane and glycosylated protein

All UniProt accessions (5): Q0VAQ4, A0A0A0MRX0, S4R3E1, S4R405, S4R466

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in epithelial cell-cell contacts. May play a role in tumor invasiveness and metastasis formation.

Subcellular location. Cell membrane. Cytoplasmic vesicle membrane.

Tissue specificity. Detected in breast, endometrium, colon and biliary tract. Detected in polarized epithelial structures characterized by cell-cell adhesion (at protein level).

Post-translational modifications. O-glycosylated. The O-glycan is modified with sialic acid residues.

Similarity. Belongs to the SMAGP family.

RefSeq proteins (2): NP_001026798, NP_001029045 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR043243	SMAGP	Family

UniProt features (12 total): glycosylation site 8, topological domain 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q0VAQ4-F1	71.58	0.25

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 (8): 17, 23, 2, 3, 6, 7, 9, 16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 187 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, LUCAS_HNF4A_TARGETS_UP, CHANDRAN_METASTASIS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, MODULE_88, PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP, PETROVA_PROX1_TARGETS_UP, MODULE_60, BOQUEST_STEM_CELL_DN, MODULE_38, CROMER_TUMORIGENESIS_DN, MODULE_104, CTGAGCC_MIR24, MODULE_55, MODULE_23

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): nucleoplasm (GO:0005654), plasma membrane (GO:0005886), cell junction (GO:0030054), cytoplasmic vesicle membrane (GO:0030659), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
binding	1
nuclear lumen	1
membrane	1
cell periphery	1
vesicle membrane	1
cytoplasmic vesicle	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

358 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SMAGP	PRAMEF19	Q5SWL8	479
SMAGP	TMEM222	Q9H0R3	476
SMAGP	TSNAXIP1	Q2TAA8	435
SMAGP	ANKRD22	Q5VYY1	405
SMAGP	MITD1	Q8WV92	403
SMAGP	RELN	P78509	384
SMAGP	NKTR	P30414	379
SMAGP	C7orf25	Q9BPX7	378
SMAGP	WDR5B	Q86VZ2	359
SMAGP	SLC25A26	Q70HW3	359
SMAGP	SPATA4	Q8NEY3	344
SMAGP	COX19	Q49B96	323
SMAGP	CEACAM20	Q6UY09	321
SMAGP	WWC3	Q9ULE0	310
SMAGP	SLC4A8	Q2Y0W8	310

IntAct

115 interactions, top by confidence:

A	B	Type	Score
SMAGP	SGTA	psi-mi:“MI:0915”(physical association)	0.560
SGTA	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	SUSD3	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	PIGP	psi-mi:“MI:0915”(physical association)	0.560
PLPP6	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
OPRD1	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	TMEM106C	psi-mi:“MI:0915”(physical association)	0.560
ATP1B3	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
OPRM1	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
PIGP	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	GPX8	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	REEP4	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	ARL13B	psi-mi:“MI:0915”(physical association)	0.560
CD53	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	RNASEK	psi-mi:“MI:0915”(physical association)	0.560
UPK2	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	TMX2	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	TMEM14B	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	SLC10A6	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	PLPPR2	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	TMEM80	psi-mi:“MI:0915”(physical association)	0.560
FFAR2	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
C2orf74	SMAGP	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	TMEM45B	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	TMEM51	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	SPACA1	psi-mi:“MI:0915”(physical association)	0.560
SMAGP	JAGN1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (42): SMAGP (Two-hybrid), SMAGP (Reconstituted Complex), SMAGP (Affinity Capture-RNA), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid), SMAGP (Two-hybrid)

ESM2 similar proteins: A0A1B0GW64, A2AFR3, A4IFL2, A6QLZ5, A8MVS5, A8MWV9, E1BBQ2, E9Q2Z6, O54693, O73612, P01134, P0C8R9, P18519, P48030, P52795, P52796, P98172, Q0VAQ4, Q0VBP7, Q14CM0, Q15223, Q3MHZ5, Q4FZH1, Q4R566, Q5JRV8, Q5R8M2, Q5RB29, Q5T1S8, Q5T292, Q5VX71, Q6AYP5, Q7TPF1, Q8BHW5, Q8BR63, Q8CA71, Q8IVY1, Q8R5M8, Q91WM6, Q91XV6, Q96DD7

Diamond homologs: A4IFL2, Q0VAQ4, Q28F36, Q7TPF1, Q99KC7, Q6XFR6, Q78HU7, B3MKS0, O08775, O95727, P04921, P35918, Q0V8S9, Q0V8T0, Q0V8T3, Q0V8T4, Q0V8T6, Q0V8T8, Q0V8T9, Q149L7, Q1WIM1, Q1WIM2, Q1WIM3, Q4VA61, Q5RD64, Q640U3, Q66KX2, Q6AYP5, Q6DJ83, Q7TQM3, Q7ZXX1, Q8BLQ9, Q8N126, Q8N3J6, Q8N441, Q8NFZ8, Q8R464, Q8R5M8, Q8TDY8, Q8WYK1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

669 predictions. Top by Δscore:

Variant	Effect	Δscore
12:51246117:CAA:C	acceptor_gain	1.0000
12:51246117:CAACT:C	acceptor_gain	1.0000
12:51246120:C:CC	acceptor_gain	1.0000
12:51246121:T:C	acceptor_gain	1.0000
12:51246121:T:TC	acceptor_gain	1.0000
12:51246839:A:AC	acceptor_gain	1.0000
12:51246839:A:C	acceptor_gain	1.0000
12:51246841:G:GC	acceptor_gain	1.0000
12:51246849:G:C	acceptor_gain	1.0000
12:51246849:G:GC	acceptor_gain	1.0000
12:51246085:C:CT	acceptor_gain	0.9900
12:51246086:G:T	acceptor_gain	0.9900
12:51246091:C:CT	acceptor_gain	0.9900
12:51246829:CTT:C	acceptor_gain	0.9900
12:51246832:C:CC	acceptor_gain	0.9900
12:51269240:CCTA:C	donor_loss	0.9900
12:51269241:CTAC:C	donor_loss	0.9900
12:51269242:TAC:T	donor_loss	0.9900
12:51269243:ACC:A	donor_loss	0.9900
12:51269244:C:CT	donor_loss	0.9900
12:51269244:CCT:C	donor_gain	0.9900
12:51246833:T:A	acceptor_loss	0.9800
12:51269239:ACCT:A	donor_loss	0.9800
12:51269452:C:A	donor_gain	0.9800
12:51246115:AACAA:A	acceptor_gain	0.9700
12:51246745:TATTA:T	donor_loss	0.9700
12:51246746:ATTAC:A	donor_loss	0.9700
12:51246747:TTACC:T	donor_loss	0.9700
12:51246748:TACC:T	donor_loss	0.9700
12:51246749:A:AT	donor_loss	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000154132 (12:51250750 T>A), RS1000680074 (12:51270113 G>C), RS1000698375 (12:51244202 TTTTA>T), RS1000906103 (12:51268641 G>A), RS1000976882 (12:51256645 A>G), RS1001108702 (12:51250149 C>A,G,T), RS1001210285 (12:51265906 C>A), RS1001281044 (12:51264759 C>T), RS1001288078 (12:51249909 G>A), RS1001313605 (12:51262141 A>G), RS1001394695 (12:51258778 T>C), RS1001496638 (12:51255928 T>C,G), RS1001566174 (12:51249826 A>G), RS1001611711 (12:51250343 C>G), RS1001632632 (12:51245258 A>G)

Disease associations

OMIM: gene MIM:621255 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90002395_128	Mean platelet volume	3.000000e-78

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression	6
sodium arsenite	increases abundance, increases expression, affects cotreatment	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Arsenic	affects cotreatment, increases expression, decreases expression, increases abundance	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tretinoin	increases expression, decreases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	decreases expression	1
sodium arsenate	decreases expression, increases abundance	1
2-methyl-4-isothiazolin-3-one	increases expression	1
trichostatin A	increases expression	1
arsenite	increases methylation	1
manganese chloride	decreases expression, increases abundance, affects cotreatment, increases expression	1
cupric chloride	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
2-palmitoylglycerol	increases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	increases expression	1
(+)-JQ1 compound	decreases expression	1
Decitabine	affects expression	1
Sunitinib	decreases expression	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Carbamazepine	affects expression	1

Clinical trials (associated diseases)

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