CD53

Summary

CD53 (CD53 molecule, HGNC:1686) is a protein-coding gene on chromosome 1p13.3, encoding Leukocyte surface antigen CD53 (P19397). Structural component of specialized membrane microdomains known as tetraspanin-enriched microdomains (TERMs), which act as platforms for receptor clustering and signaling.

The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. It contributes to the transduction of CD2-generated signals in T cells and natural killer cells and has been suggested to play a role in growth regulation. Familial deficiency of this gene has been linked to an immunodeficiency associated with recurrent infectious diseases caused by bacteria, fungi and viruses. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 963 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 34 total
• GTEx eGene: eQTL in 12 tissues, sQTL in 0 (q < 0.05)
• Constraint (gnomAD): pLI 0.04 (LoF-tolerant), LOEUF 0.91 (unconstrained)
• MANE Select transcript: NM_000560

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1686
Approved symbol	CD53
Name	CD53 molecule
Location	1p13.3
Locus type	gene with protein product
Status	Approved
Aliases	TSPAN25
Ensembl gene	ENSG00000143119
Ensembl biotype	protein_coding
OMIM	151525
Entrez	963

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 25 protein_coding, 4 protein_coding_CDS_not_defined

MANE Select: ENST00000271324

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 2, TSL 5: 2

ENST00000271324, ENST00000464329, ENST00000471220, ENST00000476408, ENST00000497404, ENST00000648608, ENST00000897406, ENST00000897407, ENST00000897408, ENST00000897409, ENST00000897410, ENST00000897411, ENST00000897412, ENST00000897413, ENST00000897414, ENST00000897415, ENST00000897416, ENST00000897417, ENST00000897418, ENST00000897419, ENST00000897420, ENST00000922910, ENST00000922911, ENST00000922912, ENST00001099572, ENST00001099573, ENST00001099574, ENST00001099575, ENST00001145357

RefSeq mRNA: 3 — MANE Select: NM_000560 NM_000560, NM_001040033, NM_001320638

CCDS: CCDS829

Canonical transcript exons

ENST00000271324 — 8 exons

Exon	Start	End
ENSE00000958193	110897809	110897892
ENSE00001933244	110873148	110873248
ENSE00003568180	110894960	110895055
ENSE00003568424	110892345	110892533
ENSE00003625024	110894327	110894401
ENSE00003639112	110891392	110891471
ENSE00003684533	110896653	110896733
ENSE00004028294	110899124	110899922

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 99.57.

FANTOM5 (CAGE): breadth broad, TPM avg 101.9476 / max 3153.7797, expressed in 661 samples.

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

Genetic regulation across tissues (GTEx eQTL / sQTL)

CD53 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 12 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

12 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Brain Cortex	eqtl	1.6e-15	+0.52	1:110875293:C:A
Brain Frontal Cortex BA9	eqtl	1.6e-13	+0.42	1:110849689:A:G
Cells EBV-transformed lymphocytes	eqtl	1.3e-06	-0.21	1:110898251:C:T
Skin Not Sun Exposed Suprapubic	eqtl	1.0e-05	-0.13	1:110898251:C:T
Testis	eqtl	3.0e-04	+0.20	1:110954964:C:T
Adipose Subcutaneous	eqtl	1.7e-03	-0.07	1:110887038:C:T
Spleen	eqtl	2.2e-03	-0.17	1:110886721:T:C
Nerve Tibial	eqtl	6.0e-03	-0.07	1:110901756:G:A
Esophagus Muscularis	eqtl	1.4e-02	+0.06	1:110828087:C:T
Skin Sun Exposed Lower leg	eqtl	1.6e-02	-0.07	1:110889113:AT:A
Brain Spinal cord cervical c-1	eqtl	2.2e-02	-1.25	1:110282725:C:T
Colon Transverse	eqtl	4.8e-02	+0.06	1:111590956:A:T

FANTOM5 promoters

10 alternative TSS:

Promoter ID	TPM avg	Samples expressed
4581	80.3215	623
4582	13.4259	558
4578	2.8520	118
4583	1.9732	383
4580	1.9021	367
4579	0.9599	173
4590	0.1685	93
4589	0.1407	56
4584	0.1077	63
4588	0.0962	48

Top tissues by expression

showing 100 of 295 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	99.57	gold quality
blood	UBERON:0000178	99.57	gold quality
leukocyte	CL:0000738	99.49	gold quality
monocyte	CL:0000576	99.48	gold quality
mononuclear cell	CL:0000842	99.48	gold quality
spleen	UBERON:0002106	99.36	gold quality
vermiform appendix	UBERON:0001154	99.28	gold quality
lymph node	UBERON:0000029	98.97	gold quality
bone marrow	UBERON:0002371	98.77	gold quality
bone marrow cell	CL:0002092	98.66	gold quality
epithelium of nasopharynx	UBERON:0001951	98.31	gold quality
nasopharynx	UBERON:0001728	98.30	gold quality
caecum	UBERON:0001153	98.23	gold quality
right lung	UBERON:0002167	98.11	gold quality
upper lobe of left lung	UBERON:0008952	97.60	gold quality
trabecular bone tissue	UBERON:0002483	97.51	gold quality
upper lobe of lung	UBERON:0008948	97.43	gold quality
bone element	UBERON:0001474	97.41	gold quality
thymus	UBERON:0002370	97.36	gold quality
gall bladder	UBERON:0002110	97.23	gold quality
lower lobe of lung	UBERON:0008949	96.79	gold quality
periodontal ligament	UBERON:0008266	96.76	gold quality
rectum	UBERON:0001052	96.75	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.16	gold quality
lung	UBERON:0002048	95.61	gold quality
decidua	UBERON:0002450	95.04	gold quality
omental fat pad	UBERON:0010414	94.89	gold quality
peritoneum	UBERON:0002358	94.86	gold quality
right coronary artery	UBERON:0001625	94.46	gold quality
small intestine	UBERON:0002108	94.39	gold quality
superficial temporal artery	UBERON:0001614	94.37	gold quality
adipose tissue of abdominal region	UBERON:0007808	94.21	gold quality
inferior vagus X ganglion	UBERON:0005363	93.74	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.58	gold quality
tonsil	UBERON:0002372	93.46	gold quality
smooth muscle tissue	UBERON:0001135	93.41	gold quality
colonic epithelium	UBERON:0000397	93.35	gold quality
mucosa of urinary bladder	UBERON:0001259	93.32	gold quality
spinal cord	UBERON:0002240	93.15	gold quality
pylorus	UBERON:0001166	93.14	gold quality
palpebral conjunctiva	UBERON:0001812	92.90	gold quality
diaphragm	UBERON:0001103	92.60	silver quality
left uterine tube	UBERON:0001303	92.41	gold quality
cervix squamous epithelium	UBERON:0006922	92.14	gold quality
visceral pleura	UBERON:0002401	91.95	gold quality
pericardium	UBERON:0002407	91.85	gold quality
descending thoracic aorta	UBERON:0002345	91.83	gold quality
mucosa of transverse colon	UBERON:0004991	91.81	gold quality
synovial joint	UBERON:0002217	91.74	gold quality
pleura	UBERON:0000977	91.48	gold quality
olfactory bulb	UBERON:0002264	91.36	silver quality
transverse colon	UBERON:0001157	91.06	gold quality
coronary artery	UBERON:0001621	90.84	gold quality
left coronary artery	UBERON:0001626	90.84	gold quality
cardia of stomach	UBERON:0001162	90.78	gold quality
parietal pleura	UBERON:0002400	90.73	gold quality
intestine	UBERON:0000160	90.70	gold quality
type B pancreatic cell	CL:0000169	90.66	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.66	gold quality
layer of synovial tissue	UBERON:0007616	90.55	gold quality
duodenum	UBERON:0002114	90.48	gold quality
thoracic aorta	UBERON:0001515	90.47	gold quality
ascending aorta	UBERON:0001496	90.25	gold quality
right adrenal gland cortex	UBERON:0035827	90.22	gold quality
right adrenal gland	UBERON:0001233	90.17	gold quality
placenta	UBERON:0001987	90.12	gold quality
minor salivary gland	UBERON:0001830	90.11	gold quality
germinal epithelium of ovary	UBERON:0001304	90.07	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.06	gold quality
subcutaneous adipose tissue	UBERON:0002190	89.98	gold quality
left adrenal gland	UBERON:0001234	89.97	gold quality
trigeminal ganglion	UBERON:0001675	89.93	gold quality
left adrenal gland cortex	UBERON:0035825	89.91	gold quality
large intestine	UBERON:0000059	89.73	gold quality
ileal mucosa	UBERON:0000331	89.73	gold quality
amniotic fluid	UBERON:0000173	89.67	gold quality
jejunal mucosa	UBERON:0000399	89.67	gold quality
colon	UBERON:0001155	89.49	gold quality
urinary bladder	UBERON:0001255	89.36	gold quality
cervix epithelium	UBERON:0004801	89.34	gold quality
adrenal cortex	UBERON:0001235	89.18	gold quality
adipose tissue	UBERON:0001013	89.13	gold quality
peripheral nervous system	UBERON:0000010	89.11	gold quality
tibial nerve	UBERON:0001323	89.11	gold quality
body of stomach	UBERON:0001161	89.05	gold quality
subthalamic nucleus	UBERON:0001906	88.86	gold quality
saliva-secreting gland	UBERON:0001044	88.58	gold quality
fundus of stomach	UBERON:0001160	88.55	gold quality
adrenal gland	UBERON:0002369	88.48	gold quality
connective tissue	UBERON:0002384	88.45	gold quality
eye	UBERON:0000970	88.34	gold quality
colonic mucosa	UBERON:0000317	88.29	gold quality
substantia nigra	UBERON:0002038	88.26	gold quality
mammary duct	UBERON:0001765	88.23	gold quality
mouth mucosa	UBERON:0003729	88.23	gold quality
metanephros cortex	UBERON:0010533	88.22	gold quality
skin of hip	UBERON:0001554	88.21	gold quality
midbrain	UBERON:0001891	88.19	gold quality
mucosa of stomach	UBERON:0001199	88.14	gold quality
epithelium of mammary gland	UBERON:0003244	87.87	gold quality

Single-cell (SCXA)

Detected in 22 experiment(s), a significant marker in 18.

Experiment	Marker?	Max mean expression
E-GEOD-75688	yes	790.80
E-HCAD-1	yes	114.08
E-MTAB-6701	yes	96.07
E-MTAB-8142	yes	80.85
E-GEOD-135922	yes	45.42
E-GEOD-84465	yes	43.04
E-MTAB-8410	yes	38.70
E-MTAB-10287	yes	37.77
E-GEOD-134144	yes	32.13
E-HCAD-10	yes	24.37
E-HCAD-9	yes	19.84
E-CURD-112	yes	18.65
E-HCAD-11	yes	17.11
E-MTAB-10042	yes	13.16
E-GEOD-137537	yes	5.40

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 78 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Tonsil	tissue	419.9	high
Lymph node	tissue	372.2	high
Appendix	tissue	268.3	high
Spleen	tissue	207.0	high
Thymus	tissue	135.1
Bone marrow	tissue	119.6	low
Lung	tissue	108.4	medium
Urinary bladder	tissue	79.6	medium
Adipose tissue	tissue	59.3	low
Placenta	tissue	54.9	medium
Gallbladder	tissue	54.8	low
Smooth muscle	tissue	52.1	low
Rectum	tissue	51.4	low
Small intestine	tissue	48.8	low
Liver	tissue	43.7	low
Stomach 1	tissue	41.7	low
Spinal cord	tissue	41.4
Hypothalamus	tissue	40.0
Colon	tissue	38.9	low
Substantia nigra	tissue	38.3
Periaqueductal gray	tissue	38.3
Pons	tissue	36.2
Duodenum	tissue	35.7	not detected
Medulla oblongata	tissue	34.5
Corpus callosum	tissue	34.5
Midbrain	tissue	31.3
Septum	tissue	31.0
Adrenal gland	tissue	29.1	medium
Breast	tissue	25.3	low
Thalamus	tissue	25.2
Superior colliculi	tissue	23.7
Putamen	tissue	22.6
Cervix	tissue	19.5	medium
Ventral forebrain	tissue	19.2
Hippocampal formation	tissue	19.0
Amygdala	tissue	18.9
Esophagus	tissue	18.8	medium
Caudate putamen	tissue	18.8
Salivary gland	tissue	18.2	medium
Choroid plexus	tissue	16.8
Endometrium 1	tissue	16.2	medium
Basal ganglia	tissue	16.2	medium
Fallopian tube	tissue	15.9	not detected
Frontal cortex	tissue	15.4
Locus coeruleus	tissue	13.7
Kidney	tissue	12.4	medium
Seminal vesicle	tissue	12.0	medium
Prostate	tissue	12.0	medium
Entorhinal cortex	tissue	11.9
Heart muscle	tissue	11.4	medium
Cerebral cortex	tissue	11.2	medium
Pancreas	tissue	11.2	low
Olfactory bulb	tissue	11.2
Insular cortex	tissue	11.2
Hippocampus	tissue	11.1	low
Motor cortex	tissue	10.8
Retrosplenial cortex	tissue	10.7
Temporal cortex	tissue	10.3
Prefrontal cortex	tissue	10.0
Tongue	tissue	9.9

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Lateral funiculus (white matter) (58.5), Dorsal spinal cord (41.4), Ventral spinal cord (41.0), White matter (34.5), Blood vessel (30.9).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ETS1, SPI1

miRNA regulators (miRDB)

Targeting CD53 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 37 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-5690	99.25	67.58	1012
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-8070	99.07	69.30	1303
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-224-3P	98.91	68.42	1815
HSA-MIR-522-3P	98.91	68.56	1817
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-374A-3P	98.87	67.82	1531
HSA-MIR-412-3P	98.86	66.89	712
HSA-MIR-6754-3P	98.84	66.60	889
HSA-MIR-3945	98.68	64.21	553
HSA-MIR-6764-3P	98.44	67.64	1153
HSA-MIR-6824-3P	98.44	67.62	1154
HSA-MIR-758-3P	98.42	68.60	1122
HSA-MIR-653-3P	98.31	67.71	1542
HSA-MIR-6882-3P	98.23	67.01	1119

Functional genomics

gnomAD constraint: pLI 0.0401, LOEUF 0.912, missense Z 1.21 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000271324 — one region, missense o/e 0.82.

Literature-anchored findings (GeneRIF, showing 10)

• Ligation of CD53 triggers a survival response and reduces the number of cells that enter apoptosis. The CD53 antigen interactions might contribute to cell survival in poorly vascularized regions of the tumor mass. (PMID:12606948)
• Analysis of lymphocyte subsets showed that the total number of CD3+, CD4+, CD8+ and CD56+ lymphocytes increased after the intensive protocol before falling below pre-exercise values at 1 h post-exercise. (PMID:16506060)
• The paradox is that lymphocytes from RA patients are believed to resist apoptosis, and we suggest that the elevated expression of CD53, which results from the increased oxidative stress, may protect against apoptosis. (PMID:17210617)
• SNP rs6679497 in gene CD53 showed significant association with TNFalpha levels (P=0.001); no association of this SNP was observed with osteoarthritis (PMID:20407468)
• CD53 is associated with population asthma risk via the functional promoter polymorphism -1560 C>T. (PMID:23313165)
• In this study, significant and lineage-dependent association of CD53 locus with Tuberculosis (TB) onset was identified from the pathogen lineage-based genome-wide association study (GWAS). (PMID:28878339)
• Eight SNPs of CD53 were found to be associated with tuberculosis case. (PMID:30506122)
• Tetraspanin CD53: an overlooked regulator of immune cell function. (PMID:32440787)
• Open conformation of tetraspanins shapes interaction partner networks on cell membranes. (PMID:32974937)
• The conformation of tetraspanins CD53 and CD81 differentially affects their nanoscale organization and interaction with their partners. (PMID:39159818)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:64051	ENSDARG00000068233
mus_musculus	Cd53	ENSMUSG00000040747
rattus_norvegicus	Cd53	ENSRNOG00000017874

Paralogs (32): TSPAN6 (ENSG00000000003), CD9 (ENSG00000010278), TSPAN9 (ENSG00000011105), TSPAN17 (ENSG00000048140), TSPAN32 (ENSG00000064201), CD82 (ENSG00000085117), TSPAN15 (ENSG00000099282), CD37 (ENSG00000104894), UPK1A (ENSG00000105668), TSPAN12 (ENSG00000106025), TSPAN13 (ENSG00000106537), TSPAN14 (ENSG00000108219), CD81 (ENSG00000110651), TSPAN11 (ENSG00000110900), PRPH2 (ENSG00000112619), UPK1B (ENSG00000114638), TSPAN1 (ENSG00000117472), TSPAN8 (ENSG00000127324), TSPAN16 (ENSG00000130167), TSPAN2 (ENSG00000134198), CD63 (ENSG00000135404), TSPAN31 (ENSG00000135452), TSPAN3 (ENSG00000140391), ROM1 (ENSG00000149489), TSPAN7 (ENSG00000156298), TSPAN18 (ENSG00000157570), TSPAN33 (ENSG00000158457), TSPAN5 (ENSG00000168785), CD151 (ENSG00000177697), TSPAN10 (ENSG00000182612), TSPAN4 (ENSG00000214063), TSPAN19 (ENSG00000231738)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:88341) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 1 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal B cell physiology	1

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.

Organism	UniProt	Identity	Method
Pan troglodytes	P60034	100.0%	Diamond
Chlorocebus aethiops	P61170	100.0%	Diamond
Macaca mulatta	P61171	100.0%	Diamond
Bos taurus	Q17QJ5	99.6%	Diamond
Pongo abelii	Q5RAP3	99.2%	Diamond
Xenopus tropicalis	B0BM39	98.7%	Diamond
Xenopus laevis	Q6DCQ3	98.7%	Diamond
Saguinus oedipus	Q9N0J9	97.9%	Diamond
Sus scrofa	Q06AA5	97.1%	Diamond
Ovis aries	B3VSC2	94.6%	Diamond
Felis catus	Q76B49	89.9%	Diamond
Oryctolagus cuniculus	Q28709	87.8%	Diamond
Gallus gallus	A0A8V0ZLT4	81.0%	Diamond
Salmo salar	B5X3I6	78.2%	Diamond
Caenorhabditis elegans	Q22495	44.9%	Diamond
Schistosoma japonicum	P91799	30.8%	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).

Symbol	Type	Entrez
CEPT1	protein-coding	10390
DRAM2	protein-coding	128338
LRIF1	protein-coding	55791
DENND2D	protein-coding	79961

Protein

Protein identifiers

Leukocyte surface antigen CD53 — P19397 (reviewed: P19397)

Alternative names: Cell surface glycoprotein CD53, Tetraspanin-25

All UniProt accessions (2): B4DQB5, P19397

UniProt curated annotations — full annotation on UniProt →

Function. Structural component of specialized membrane microdomains known as tetraspanin-enriched microdomains (TERMs), which act as platforms for receptor clustering and signaling. Participates thereby in diverse biological functions such as cell signal transduction, adhesion, migration and protein trafficking. Plays a role in the activation of monocytes and B-cells. Acts as an essential regulator of B-cell development by promoting interleukin-7 receptor/IL7R signaling. Also promotes, in B-cells, the BCR signaling by recruiting PKC to the plasma membrane in order to phosphorylate its substrates. Plays an essential role in B- and T-cells homing to lymph nodes by stabilizing L-selectin/SELL cell surface expression. Also mediates metabolic and inflammatory functions in hepatocytes and adipose tissue by promoting TNF and LPS signaling independent of the immune compartment.

Subunit / interactions. Interacts with SCIMP. Interacts with CD45/PTPRC. Interacts with IL7R. Interacts with RBL2 and PPP2CA.

Subcellular location. Cell membrane. Cell junction. Membrane. Synapse.

Tissue specificity. B-cells, monocytes, macrophages, neutrophils, single (CD4 or CD8) positive thymocytes and peripheral T-cells.

Similarity. Belongs to the tetraspanin (TM4SF) family.

RefSeq proteins (3): NP_000551, NP_001035122, NP_001307567 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000301	Tetraspanin_animals	Family
IPR008952	Tetraspanin_EC2_sf	Homologous_superfamily
IPR018499	Tetraspanin/Peripherin	Family
IPR018503	Tetraspanin_CS	Conserved_site

Pfam: PF00335

UniProt features (26 total): helix 9, topological domain 5, transmembrane region 4, glycosylation site 2, mutagenesis site 2, strand 2, chain 1, turn 1

Structure

Experimental structures (PDB)

1 structures by resolution:

PDB	Title	Method	Resolution (Å)
6WVG	human CD53	X-RAY DIFFRACTION	2.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P19397-F1	93.05	0.86

Human Protein Atlas

Protein class: CD markers, Transporters, Accessory Factors Involved in Transport, Predicted membrane proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH enhanced

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 (2)

Type	Positions
N-linked (glcnac…) asparagine	129, 148

Mutagenesis-validated functional residues (2)

Position	Phenotype
43	about 50% loss of b-cell chemotactic activity.
44	about 50% loss of b-cell chemotactic activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 3; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

3 pathways:

ID	Pathway	Evidence
R-HSA-6798695	Neutrophil degranulation	curated
R-HSA-168256	Immune System	—
R-HSA-168249	Innate Immune System	—

MSigDB gene sets: 274 (showing top): RNGTGGGC_UNKNOWN, WALLACE_PROSTATE_CANCER_RACE_UP, REACTOME_INNATE_IMMUNE_SYSTEM, MCLACHLAN_DENTAL_CARIES_UP, GOCC_SECRETORY_GRANULE, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, MODULE_45, MODULE_64, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, LANG_MYB_FAMILY_TARGETS, KYNG_DNA_DAMAGE_DN, MODULE_16, WIELAND_UP_BY_HBV_INFECTION, HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP, MODULE_118

GO Biological Process (3): signal transduction (GO:0007165), receptor clustering (GO:0043113), positive regulation of myoblast fusion (GO:1901741)

GO Molecular Function (3): identical protein binding (GO:0042802), protein-membrane adaptor activity (GO:0043495), protein binding (GO:0005515)

GO Cellular Component (9): immunological synapse (GO:0001772), plasma membrane (GO:0005886), cell-cell junction (GO:0005911), specific granule membrane (GO:0035579), synapse (GO:0045202), extracellular exosome (GO:0070062), tertiary granule membrane (GO:0070821), membrane (GO:0016020), anchoring junction (GO:0070161)

Reactome top-level categories

2 top-level categories:

Category	Pathways
Innate Immune System	1
Immune System	1

GO top-level categories

22 GO namespaces:

Category	Terms
plasma membrane	2
cellular anatomical structure	2
secretory granule membrane	2
cell junction	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
protein localization to membrane	1
myoblast fusion	1
positive regulation of syncytium formation by plasma membrane fusion	1
regulation of myoblast fusion	1
protein binding	1
protein-macromolecule adaptor activity	1
binding	1
membrane	1
cell periphery	1
anchoring junction	1
specific granule	1
extracellular vesicle	1
tertiary granule	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 6 of 15 annotations. The rest are phylogenetic / computational / electronic (IEA).

6 experimentally-supported GO terms:

GO term	NS	Evidence
receptor clustering	BP	direct assay
extracellular exosome	CC	high-throughput assay
immunological synapse	CC	direct assay
plasma membrane	CC	direct assay
identical protein binding	MF	physical interaction
protein-membrane adaptor activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 1,388 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD53	CD101	Q93033	735
CD53	UPK1A	O00322	732
CD53	UPK1B	O75841	703
CD53	TSPAN31	Q12999	683
CD53	UPK3A	O75631	646
CD53	LAPTM5	Q13571	570
CD53	CD2	P06729	562
CD53	CD58	P19256	526
CD53	EVI2B	P34910	509
CD53	TSPAN32	Q96QS1	498
CD53	CD6	P30203	470
CD53	CD52	P31358	465
CD53	UPK2	O00526	450
CD53	ITGB2	P05107	442
CD53	CD48	P09326	442

IntAct

Human interaction partners of CD53 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 78 partners by confidence:

Partner	Interaction type	MIscore	Records
CREB3L1	physical association	0.560	5
AIG1	physical association	0.560	3
APOD	physical association	0.560	3
ARL13B	physical association	0.560	3
ASGR2	physical association	0.560	3
ATP6V0C	physical association	0.560	3
BCL2L13	physical association	0.560	3
BIK	physical association	0.560	3
BTN2A2	physical association	0.560	3
C1QL4	physical association	0.560	3
CD302	physical association	0.560	3
CD37	physical association	0.560	3
CLCN7	physical association	0.560	3
CLDN19	physical association	0.560	3
CLDN7	physical association	0.560	3
CLEC7A	physical association	0.560	3
CNIH1	physical association	0.560	3
CNIH2	physical association	0.560	3
COL4A5	physical association	0.560	3
CTXN3	physical association	0.560	3
CXCL16	physical association	0.560	3
CYBC1	physical association	0.560	3
ECE2	physical association	0.560	3
EFNA5	physical association	0.560	3
EMP1	physical association	0.560	3
ERG28	physical association	0.560	3
FAM209A	physical association	0.560	3
GET1	physical association	0.560	3
GIMAP5	physical association	0.560	3
GJA8	physical association	0.560	3

BioGRID (96 interactions; top human partners by supporting records): AIG1 (Two-hybrid), ALG14 (Affinity Capture-MS), APOD (Two-hybrid), ARL13B (Two-hybrid), ASGR2 (Two-hybrid), ATP6V0C (Two-hybrid), BCL2L13 (Two-hybrid), BIK (Two-hybrid), BTN2A2 (Two-hybrid), C14orf1 (Two-hybrid), C17orf62 (Two-hybrid), C1QL4 (Two-hybrid), C2orf82 (Two-hybrid), CD2 (Affinity Capture-Western), CD302 (Two-hybrid)

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

Complex	Subunits	Members
★ ITGA4-ITGB1-CD53 complex	3	CD53, ITGA4, ITGB1

Disease & clinical

Genetic variants

Variant evidence for CD53: 34 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	1
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 24 predictions of 587):

Position(s)	Effect	Δscore	Sites
1:110873249–110873250	donor_loss	1.0000	4
1:110891390	acceptor_loss	1.0000	3
1:110891391	acceptor_gain	1.0000
1:110891472–110891473	donor_loss	1.0000	5
1:110894942	acceptor_gain	1.0000
1:110873250	donor_loss	0.9900
1:110889105	donor_gain	0.9900
1:110891391	acceptor_loss	0.9900
1:110891857	donor_gain	0.9900
1:110892534–110892535	donor_loss	0.9900	6

AlphaMissense

498 missense substitutions predicted likely pathogenic (of 1,441 scored), across 149 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:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
F68	8	0.803	0.970
F202	8	0.797	0.954
C144	7	0.979	0.992
C161	7	0.977	0.990
C145	7	0.975	0.988
C170	7	0.974	0.989
W153	7	0.964	0.997
W135	7	0.951	0.993
F85	7	0.924	0.991
M200	7	0.912	0.982
D136	7	0.901	0.945
F86	7	0.831	0.968
D152	7	0.825	0.899
N17	7	0.786	0.978
E77	7	0.758	0.918
G146	6	0.960	0.992
G31	6	0.938	0.986
G73	6	0.929	0.990
G60	6	0.924	0.991
G70	6	0.924	0.986

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:151525 | disease phenotypes:

GWAS associations

2 associations:

Study	Trait	p-value
GCST001272_4	Cytomegalovirus antibody response	5e-6
GCST001762_353	Obesity-related traits	9e-6

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tretinoin	increases expression, increases reaction, affects cotreatment	4
Antirheumatic Agents	decreases expression	2
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
terbufos	decreases methylation	1
cobaltous chloride	increases expression	1
tamibarotene	increases expression	1
CGP 52608	affects binding, increases reaction	1
Arsenic Trioxide	affects cotreatment, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression, increases abundance	1
Calcitriol	decreases expression	1
Cisplatin	increases expression	1
Dexamethasone	increases expression	1
Diuron	decreases expression	1
Fonofos	decreases methylation	1
Parathion	decreases methylation	1
Phthalic Acids	decreases methylation	1
Dronabinol	decreases expression	1
Thiophenes	increases expression, increases reaction	1
Triclosan	decreases expression	1
Cyclosporine	increases methylation	1
Sodium Selenite	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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