CD63

gene
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Also known as ME491TSPAN30HOP-26Pltgp40AD1

Summary

CD63 (CD63 molecule, HGNC:1692) is a protein-coding gene on chromosome 12q13.2, encoding CD63 antigen (P08962). Functions as a cell surface receptor for TIMP1 and plays a role in the activation of cellular signaling cascades.

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. The encoded protein is a cell surface glycoprotein that is known to complex with integrins. It may function as a blood platelet activation marker. Deficiency of this protein is associated with Hermansky-Pudlak syndrome. Also this gene has been associated with tumor progression. Alternative splicing results in multiple transcript variants encoding different protein isoforms.

Source: NCBI Gene 967 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 49 total — 4 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 1
  • Druggable target: yes — 2 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_001780

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1692
Approved symbolCD63
NameCD63 molecule
Location12q13.2
Locus typegene with protein product
StatusApproved
AliasesME491, TSPAN30, HOP-26, Pltgp40, AD1
Ensembl geneENSG00000135404
Ensembl biotypeprotein_coding
OMIM155740
Entrez967

Gene structure

Transcript identifiers

Ensembl transcripts: 46 — 43 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000257857, ENST00000420846, ENST00000546457, ENST00000546939, ENST00000548117, ENST00000548160, ENST00000548898, ENST00000549117, ENST00000550050, ENST00000550776, ENST00000551173, ENST00000552067, ENST00000552164, ENST00000552692, ENST00000552754, ENST00000555199, ENST00000866659, ENST00000866660, ENST00000866661, ENST00000866662, ENST00000866663, ENST00000866664, ENST00000866665, ENST00000866666, ENST00000866667, ENST00000866668, ENST00000866669, ENST00000866670, ENST00000866671, ENST00000866672, ENST00000866673, ENST00000866674, ENST00000866675, ENST00000922866, ENST00000922867, ENST00000922868, ENST00000922869, ENST00000922870, ENST00000922871, ENST00000922872, ENST00000922873, ENST00000922874, ENST00000922875, ENST00000922876, ENST00000922877, ENST00000944923

RefSeq mRNA: 16 — MANE Select: NM_001780 NM_001257389, NM_001257390, NM_001257391, NM_001257392, NM_001257400, NM_001257401, NM_001267698, NM_001413281, NM_001413282, NM_001413283, NM_001413284, NM_001413285, NM_001413286, NM_001413287, NM_001413288, NM_001780

CCDS: CCDS58242, CCDS58243, CCDS8890

Canonical transcript exons

ENST00000257857 — 8 exons

ExonStartEnd
ENSE000009200775572827655728352
ENSE000015177725572895355729009
ENSE000023252615572532355725626
ENSE000034771965572612155726261
ENSE000034897555572581355725896
ENSE000035677275572715155727339
ENSE000035906095572670055726795
ENSE000036910015572689055726964

Expression profiles

Bgee: expression breadth ubiquitous, 305 present calls, max score 99.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 409.9608 / max 2987.6829, expressed in 1828 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter IDTPM avgSamples expressed
131431365.39021828
13143029.82471770
1314247.05411622
1314272.82571088
1314321.88261123
1314290.8830485
1314280.5820296
1314260.3501178
1314150.304277
1314220.271798

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225599.92gold quality
tendon of biceps brachiiUBERON:000818899.85gold quality
adult organismUBERON:000702399.79gold quality
type B pancreatic cellCL:000016999.78gold quality
islet of LangerhansUBERON:000000699.78gold quality
lower lobe of lungUBERON:000894999.77gold quality
left adrenal glandUBERON:000123499.74gold quality
olfactory bulbUBERON:000226499.74gold quality
upper lobe of lungUBERON:000894899.74gold quality
thoracic aortaUBERON:000151599.73gold quality
descending thoracic aortaUBERON:000234599.73gold quality
deciduaUBERON:000245099.73gold quality
upper lobe of left lungUBERON:000895299.73gold quality
smooth muscle tissueUBERON:000113599.72gold quality
ascending aortaUBERON:000149699.72gold quality
left adrenal gland cortexUBERON:003582599.72gold quality
right adrenal glandUBERON:000123399.71gold quality
adrenal cortexUBERON:000123599.71gold quality
cardiac atriumUBERON:000208199.71gold quality
corpus epididymisUBERON:000435999.71gold quality
right atrium auricular regionUBERON:000663199.71gold quality
gall bladderUBERON:000211099.70gold quality
adrenal glandUBERON:000236999.70gold quality
myometriumUBERON:000129699.69gold quality
coronary arteryUBERON:000162199.69gold quality
left coronary arteryUBERON:000162699.69gold quality
synovial jointUBERON:000221799.69gold quality
nasal cavity epitheliumUBERON:000538499.69gold quality
right adrenal gland cortexUBERON:003582799.69gold quality
endocervixUBERON:000045899.68gold quality

Single-cell (SCXA)

Detected in 47 experiment(s), a significant marker in 28.

ExperimentMarker?Max mean expression
E-HCAD-23yes4163.56
E-GEOD-84465yes3824.37
E-MTAB-8142yes2911.04
E-HCAD-1yes2568.79
E-GEOD-139324yes2403.00
E-MTAB-10042yes1695.24
E-MTAB-10432yes1557.93
E-CURD-88yes1508.06
E-HCAD-5yes1331.97
E-HCAD-8yes994.98
E-CURD-77yes436.86
E-HCAD-4yes213.11
E-MTAB-8410yes71.46
E-CURD-122yes69.33
E-MTAB-10553yes44.20

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): BCL6, MYC

miRNA regulators (miRDB)

12 targeting CD63, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-3617-5P99.7569.411968
HSA-MIR-64199.7569.351975
HSA-MIR-361-3P99.1966.451381
HSA-MIR-6894-5P98.7063.78809
HSA-MIR-1468-5P94.1869.04176

Literature-anchored findings (GeneRIF, showing 40)

  • Results show that AP-3 is absolutely required for the delivery of CD63 to lysosomes via the trans-Golgi network. (PMID:11907283)
  • C-kit is physically associated with transmembrane 4 superfamily proteins CD9, CD63, and CD81, that may negatively modulate c-kit and thus regulate c-kit receptor sensitivity to SLF in hematopoietic progenitors. (PMID:12036870)
  • downregulation of CD63 antigen is associated with breast tumor progression (PMID:12579280)
  • possible role in HIV-1 infections specific for macrophages (PMID:12610138)
  • Post-translational modification of CD63 may be involved in the functional and morphological changes of MHC class II compartments that occur during dendritic cell maturation (PMID:12755696)
  • relationships between the expression levels of CD61, CD63, and PAC-1 on the platelet surface and the incidences of acute rejection and tubular necrosis as well as the recovery of graft function after renal transplantation (PMID:12826159)
  • Upon platelet interaction with fibrinogen, cholesterol accumulated at the tips of filopodia and at the leading edge of spreading cells; cholesterol-rich raft aggregation was accompanied by concentration of c-Src and CD63 in these cell domains (PMID:12871315)
  • The study on CD63 included its chemistry eg. if it had and O-linked carbohydrate that was digested with O-glycanase. (PMID:12974720)
  • CD63 serves as an adaptor protein that links its interaction partners to the endocytic machinery of the cell. (PMID:14660791)
  • results suggest that CD9, CD63, CD81, and CD82 could play a role in modulating the interactions between immature DCs and their environment, slowing their migratory ability. However, only CD63 would intervene in the internalization of complex antigens (PMID:15130945)
  • Constitutive expression of CD63 may indicate that this factor does not play a direct role in thyroid carcinogenesis (PMID:15375577)
  • CD63 represents an activation-induced reinforcing element, whose triggering promotes sustained and efficient T cell activation and expansion. (PMID:15528334)
  • The linkage of CD63 with PI 4-kinase may result in the recruitment of this signaling enzyme to specific membrane locations in the platelet where it influences phosphoinositide-dependent signaling and platelet spreading. (PMID:15711748)
  • This study identifies a trafficking pathway from CD63-positive multivesicular bodies to the bacterial inclusion, a novel interaction that provides essential lipids necessary for maintenance of a productive intracellular infection. (PMID:16410552)
  • CD63 is recruited to already-budded Weibel-Palade bodies by an AP-3-dependent route (PMID:16683915)
  • CD63-syntenin-1 complex is abundant on the plasma membrane (PMID:16908530)
  • CD63 is a cell surface binding partner for TIMP-1, regulating cell survival and polarization via TIMP-1 modulation of tetraspanin/integrin signaling complex. (PMID:16917503)
  • Chronic urticaria serum-induced CD63 expression assay performed on atopic whole blood by means of tricolor flow cytometry could be the most useful tool for identification of a subset of patients with autoimmune chronic urticaria. (PMID:16918509)
  • In conclusion, using well-defined experimental conditions, the measurement of CD203c up-regulation on basophils in response to specific allergens is as reliable as CD63-BAT for the in vitro diagnosis of patients with IgE-mediated allergy. (PMID:17275019)
  • positive correlation between CD63 and erythrocyte sedimentation rate in rheumatoid arthritis (PMID:17279322)
  • Results suggest that CD63 can be a biomarker for predicting the prognosis in early stages of lung adenocarcinoma. (PMID:17350713)
  • These results suggest that chronic obstructive pulmonary disease patients have different patterns of CD63 expression and polymorphonuclear neutrophils mediator release than healthy individuals. (PMID:17390088)
  • Data show that HIV-1 envelope glycoprotein (Env) and core protein (Gag) colocalize strongly with CD63 and CD81 and less strongly with CD9, and suggest that HIV-1 promotes virus assembly and cell-cell transfer by targeting these plasma membrane proteins. (PMID:17522207)
  • There is low expression of the proteins and mRNA of ME491/CD63 and integrin alpha5 in ovarian cancer. The lower the pathological differentiation is, the more significant the loss of expression is and the more likely metastasis is. (PMID:17624082)
  • PrP(c) at the cell surface of cultured human erythroblasts is rapidly internalized through the endosomal pathway, where it colocalizes with the tetraspanin CD63. (PMID:17827389)
  • Data show that an N-terminal deletion mutant of CD63 blocks entry of CXCR4-using, T-cell tropic human immunodeficiency virus type 1 (X4 HIV-1) by suppressing CXCR4 surface expression. (PMID:18182005)
  • CD63 plays a role in the regulation of ROMK channels through its association with RPTPalpha, which in turn interacts with and activates Src family PTK, thus reducing ROMK activity. (PMID:18211905)
  • Together, our results indicate that at least in tissue culture, CD63 expression is not required for either the production or the infectivity of HIV-1. (PMID:18321974)
  • These studies confirm CD63 as a constituent in multivesicular body-to-chlamydial inclusion transport but it is not required for this association. (PMID:18426873)
  • Induction of hypercortisolism in healthy volunteers was associated with a trend toward higher expression of glycoprotein 53 on the platelet surface. (PMID:18600034)
  • CD63 is involved in granule targeting of neutrophil elastase (PMID:18669870)
  • Antigen-induced p38 MAPK phosphorylation in human basophils essentially contributes to CD63 upregulation (PMID:18727065)
  • the activation-induced degranulation of Fas ligand has distinct requirements and involves different mechanisms than those of the granule markers CD63 and CD107a/Lamp-1 (PMID:19079288)
  • Exotest for CD63+ plasma exosomes had limited sensitivity but the Exotest for detection of caveolin-1+ plasma exosomes showed a higher sensitivity. Caveolin-1+ plasma exosomes were significantly increased with respect to CD63+ exosomes in patients group (PMID:19381331)
  • CD9, CD81 and CD63 are negative regulators of HIV-1-induced cell-cell fusion. (PMID:19458002)
  • Serum sCD163 is a homogenous protein covering more than 94% of the CD163 ectodomain including the haptoglobin-hemoglobin -binding region. (PMID:19581020)
  • Surface expression of the novel CD63 variant is a distinguishing feature of mast cells, which are are stable, multiple-use cells capable of surviving and delivering several consecutive hits (PMID:20337613)
  • CD63 expression results from only the anaphylactic degranulation form of histamine release. (PMID:20633031)
  • this work provides the first evidence of a TIMP-4/CD63 association in astrocytoma tumor cells (PMID:20693981)
  • ameloblastin is expressed in osteoblasts and functions as a promoting factor for osteogenic differentiation via a novel pathway through the interaction between CD63 and integrin beta1 (PMID:21149578)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocd63ENSDARG00000025147
mus_musculusCd63ENSMUSG00000025351
rattus_norvegicusCd63ENSRNOG00000007650
drosophila_melanogasterTsp47FFBGN0033629
caenorhabditis_eleganstsp-7WBGENE00006633

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), TSPAN31 (ENSG00000135452), TSPAN3 (ENSG00000140391), CD53 (ENSG00000143119), ROM1 (ENSG00000149489), TSPAN7 (ENSG00000156298), TSPAN18 (ENSG00000157570), TSPAN33 (ENSG00000158457), TSPAN5 (ENSG00000168785), CD151 (ENSG00000177697), TSPAN10 (ENSG00000182612), TSPAN4 (ENSG00000214063), TSPAN19 (ENSG00000231738)

Protein

Protein identifiers

CD63 antigenP08962 (reviewed: P08962)

Alternative names: Granulophysin, Lysosomal-associated membrane protein 3, Lysosome integral membrane protein 1, Melanoma-associated antigen ME491, OMA81H, Ocular melanoma-associated antigen, Tetraspanin-30

All UniProt accessions (6): P08962, F8VNT9, F8VV56, F8VWK8, F8VX62, F8W022

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a cell surface receptor for TIMP1 and plays a role in the activation of cellular signaling cascades. Plays a role in the activation of ITGB1 and integrin signaling, leading to the activation of AKT, FAK/PTK2 and MAP kinases. Promotes cell survival, reorganization of the actin cytoskeleton, cell adhesion, spreading and migration, via its role in the activation of AKT and FAK/PTK2. Plays a role in VEGFA signaling via its role in regulating the internalization of KDR/VEGFR2. Plays a role in intracellular vesicular transport processes, and is required for normal trafficking of the PMEL luminal domain that is essential for the development and maturation of melanocytes. Plays a role in the adhesion of leukocytes onto endothelial cells via its role in the regulation of SELP trafficking. May play a role in mast cell degranulation in response to Ms4a2/FceRI stimulation, but not in mast cell degranulation in response to other stimuli.

Subunit / interactions. Interacts with TIMP1 and ITGB1 and recruits TIMP1 to ITGB1. Interacts with CD9. Identified in a complex with CD9 and ITGB3. Interacts with PMEL. Interacts with KDR/VEGFR2; identified in a complex with ITGB1 and KDR/VEGFR2 and is required to recruit KDR to ITGB1 complexes. Interacts with SYT7.

Subcellular location. Cell membrane. Lysosome membrane. Late endosome membrane. Endosome. Multivesicular body. Melanosome. Secreted. Extracellular exosome. Cell surface.

Tissue specificity. Detected in platelets (at protein level). Dysplastic nevi, radial growth phase primary melanomas, hematopoietic cells, tissue macrophages.

Post-translational modifications. Palmitoylated at a low, basal level in unstimulated platelets. The level of palmitoylation increases when platelets are activated by thrombin (in vitro).

Miscellaneous. Lack of expression of CD63 in platelets has been observed in a patient with Hermansky-Pudlak syndrome (HPS). Hermansky-Pudlak syndrome (HPS) is a genetically heterogeneous, rare, autosomal recessive disorder characterized by oculocutaneous albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects. This syndrome results from defects of diverse cytoplasmic organelles including melanosomes, platelet dense granules and lysosomes. Ceroid storage in the lungs is associated with pulmonary fibrosis, a common cause of premature death in individuals with HPS. This antigen is associated with early stages of melanoma tumor progression.

Similarity. Belongs to the tetraspanin (TM4SF) family.

Isoforms (3)

UniProt IDNamesCanonical?
P08962-11yes
P08962-22
P08962-33

RefSeq proteins (16): NP_001244318, NP_001244319, NP_001244320, NP_001244321, NP_001244329, NP_001244330, NP_001254627, NP_001400210, NP_001400211, NP_001400212, NP_001400213, NP_001400214, NP_001400215, NP_001400216, NP_001400217, NP_001771* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000301Tetraspanin_animalsFamily
IPR008952Tetraspanin_EC2_sfHomologous_superfamily
IPR018499Tetraspanin/PeripherinFamily
IPR018503Tetraspanin_CSConserved_site
IPR042028CD63_LELDomain

Pfam: PF00335

UniProt features (18 total): topological domain 5, transmembrane region 4, glycosylation site 3, splice variant 2, initiator methionine 1, chain 1, short sequence motif 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
9HURX-RAY DIFFRACTION1.65
9HQ5X-RAY DIFFRACTION2.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P08962-F190.820.80

Antibody-complex structures (SAbDab): 29HQ5, 9HUR

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 (3): 130, 150, 172

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-114608Platelet degranulation
R-HSA-6798695Neutrophil degranulation
R-HSA-109582Hemostasis
R-HSA-168249Innate Immune System
R-HSA-168256Immune System
R-HSA-76002Platelet activation, signaling and aggregation
R-HSA-76005Response to elevated platelet cytosolic Ca2+

MSigDB gene sets: 313 (showing top): GOBP_POTASSIUM_ION_TRANSPORT, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_EPITHELIUM_DEVELOPMENT, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_VASCULAR_ENDOTHELIAL_GROWTH_FACTOR_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, MODULE_151, REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION, MODULE_64, KAAB_HEART_ATRIUM_VS_VENTRICLE_UP, GOBP_REGULATION_OF_EPITHELIAL_CELL_MIGRATION, GOCC_CELL_SURFACE, MODULE_128

GO Biological Process (16): positive regulation of receptor internalization (GO:0002092), cell-matrix adhesion (GO:0007160), negative regulation of epithelial cell migration (GO:0010633), protein transport (GO:0015031), cell migration (GO:0016477), epithelial cell differentiation (GO:0030855), endosome to melanosome transport (GO:0035646), positive regulation of cell adhesion (GO:0045785), pigment granule maturation (GO:0048757), regulation of vascular endothelial growth factor signaling pathway (GO:1900746), regulation of potassium ion transmembrane transport (GO:1901379), positive regulation of integrin-mediated signaling pathway (GO:2001046), cell differentiation (GO:0030154), pigmentation (GO:0043473), positive regulation of endocytosis (GO:0045807), pigment cell differentiation (GO:0050931)

GO Molecular Function (2): protein-containing complex binding (GO:0044877), protein binding (GO:0005515)

GO Cellular Component (22): obsolete extracellular space (GO:0005615), nucleoplasm (GO:0005654), lysosomal membrane (GO:0005765), plasma membrane (GO:0005886), cell surface (GO:0009986), endosome membrane (GO:0010008), platelet dense granule membrane (GO:0031088), late endosome membrane (GO:0031902), endosome lumen (GO:0031904), multivesicular body membrane (GO:0032585), protein-containing complex (GO:0032991), azurophil granule membrane (GO:0035577), melanosome (GO:0042470), extracellular exosome (GO:0070062), multivesicular body, internal vesicle (GO:0097487), extracellular region (GO:0005576), lysosome (GO:0005764), endosome (GO:0005768), late endosome (GO:0005770), multivesicular body (GO:0005771), membrane (GO:0016020), vesicle (GO:0031982)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Response to elevated platelet cytosolic Ca2+1
Innate Immune System1
Immune System1
Hemostasis1
Platelet activation, signaling and aggregation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
endosome3
cell differentiation2
binding2
secretory granule membrane2
late endosome2
multivesicular body2
regulation of receptor internalization1
receptor internalization1
positive regulation of receptor-mediated endocytosis1
cell-substrate adhesion1
epithelial cell migration1
regulation of epithelial cell migration1
negative regulation of cell migration1
negative regulation of multicellular organismal process1
transport1
intracellular protein localization1
establishment of protein localization1
cell motility1
epithelium development1
endosome to pigment granule transport1
cell adhesion1
regulation of cell adhesion1
positive regulation of cellular process1
developmental maturation1
cellular pigment accumulation1
pigment cell differentiation1
regulation of signal transduction1
vascular endothelial growth factor signaling pathway1
regulation of cellular response to vascular endothelial growth factor stimulus1
regulation of potassium ion transport1
potassium ion transmembrane transport1
regulation of monoatomic cation transmembrane transport1
integrin-mediated signaling pathway1
positive regulation of signal transduction1
regulation of integrin-mediated signaling pathway1
cellular developmental process1
biological_process1
endocytosis1
regulation of endocytosis1

Protein interactions and networks

STRING

3276 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CD63TSG101Q99816998
CD63SDCBPO00560995
CD63CD81P18582992
CD63SDCBP2Q9H190992
CD63ITGB1P05556992
CD63TIMP1P01033990
CD63CD9P21926988
CD63LAMP2P13473986
CD63LAMP1P11279984
CD63CD82P27701982
CD63ANXA2P07355982
CD63HSPA4P34932981
CD63FLOT1O75955945
CD63CD151P48509935
CD63EGFRP00533867

IntAct

106 interactions, top by confidence:

ABTypeScore
CD9ADAM10psi-mi:“MI:0914”(association)0.750
TIMP1CD63psi-mi:“MI:0915”(physical association)0.690
CD63TIMP1psi-mi:“MI:0915”(physical association)0.690
TIMP1CD63psi-mi:“MI:0403”(colocalization)0.690
TIMP1CD63psi-mi:“MI:0914”(association)0.690
TIMP1CD63psi-mi:“MI:0407”(direct interaction)0.690
RETREG3PLSCR1psi-mi:“MI:0914”(association)0.640
CD63TMEM80psi-mi:“MI:0915”(physical association)0.560
TSPAN2TSPAN3psi-mi:“MI:0914”(association)0.530
LGALS3PODXLpsi-mi:“MI:0914”(association)0.530
CLGNNPC1psi-mi:“MI:0914”(association)0.530
CDS1TSPAN6psi-mi:“MI:0914”(association)0.530
MFSD4AHIP1Rpsi-mi:“MI:0914”(association)0.530
SLC5A9CD63psi-mi:“MI:0914”(association)0.530
CD63LGALS8psi-mi:“MI:0914”(association)0.530
CD63envpsi-mi:“MI:0915”(physical association)0.500
envCD63psi-mi:“MI:2364”(proximity)0.500
CD63envpsi-mi:“MI:2364”(proximity)0.500
WLSCD63psi-mi:“MI:0915”(physical association)0.490
ITGB1CD63psi-mi:“MI:0915”(physical association)0.460
CD63ITGB1psi-mi:“MI:0403”(colocalization)0.460
CD63LMP1psi-mi:“MI:0403”(colocalization)0.460
LMP1CD63psi-mi:“MI:0403”(colocalization)0.460

BioGRID (139): SDC1 (Reconstituted Complex), SDCBP (Reconstituted Complex), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (Affinity Capture-MS), CD63 (PCA), CD63 (Affinity Capture-MS)

ESM2 similar proteins: O43657, O46101, O60635, O70352, O70401, O75508, P08962, P0C672, P19331, P19397, P27591, P27701, P28648, P34285, P40237, P41731, P41732, P91799, Q11098, Q22495, Q24188, Q26499, Q28709, Q2KIS9, Q32KU6, Q3MHK4, Q3T0S3, Q4R3L1, Q4R7W6, Q55CV4, Q55CV5, Q55CV7, Q55CW7, Q58DM3, Q5RAS5, Q5RC27, Q5REK8, Q5WRN1, Q60771, Q61451

Diamond homologs: A0A8M2B5N2, A0A8V0ZLT4, A1L157, B0BM39, B3VSC2, B5X3I6, H2L006, O14817, O35566, O70352, O75954, O97703, P08962, P19075, P19397, P24485, P27701, P28648, P30932, P35762, P40237, P41731, P48509, P60033, P60034, P61170, P61171, Q06AA5, Q0VC33, Q28709, Q3ZBH3, Q3ZCD0, Q568Y5, Q58CY8, Q58DM3, Q5R9S6, Q5RAP3, Q61451, Q62745, Q6AYR9

SIGNOR signaling

1 interactions.

AEffectBMechanism
TFE3“up-regulates quantity by expression”CD63“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 101 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Neutrophil degranulation114.9×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic1
Uncertain significance26
Likely benign5
Benign2

Top pathogenic / likely-pathogenic (5)

Variant IDHGVSClassification
1452620NM_002905.5(RDH5):c.632_633del (p.Pro211fs)Pathogenic
8006NM_002905.5(RDH5):c.880G>C (p.Ala294Pro)Pathogenic
812394NM_002905.5(RDH5):c.718dup (p.Ala240fs)Pathogenic
866580NM_002905.5(RDH5):c.625C>T (p.Arg209Ter)Pathogenic
3370439NM_002905.5(RDH5):c.713G>C (p.Gly238Ala)Likely pathogenic

SpliceAI

981 predictions. Top by Δscore:

VariantEffectΔscore
12:55725639:A:Cacceptor_gain1.0000
12:55725807:TCTTA:Tdonor_loss1.0000
12:55725808:CTTA:Cdonor_loss1.0000
12:55725809:TTACC:Tdonor_loss1.0000
12:55725810:TACC:Tdonor_loss1.0000
12:55725811:A:ACdonor_gain1.0000
12:55725811:ACCTC:Adonor_loss1.0000
12:55725812:C:CCdonor_gain1.0000
12:55725812:CCT:Cdonor_gain1.0000
12:55725892:CAGCC:Cacceptor_gain1.0000
12:55725893:AGCC:Aacceptor_gain1.0000
12:55725894:GCC:Gacceptor_gain1.0000
12:55725895:CC:Cacceptor_gain1.0000
12:55725895:CCC:Cacceptor_gain1.0000
12:55725896:CC:Cacceptor_gain1.0000
12:55725897:C:CCacceptor_gain1.0000
12:55725897:C:CGacceptor_loss1.0000
12:55725897:C:Tacceptor_gain1.0000
12:55725898:T:Aacceptor_loss1.0000
12:55725903:G:Cacceptor_gain1.0000
12:55725903:G:GCacceptor_gain1.0000
12:55725907:C:CTacceptor_gain1.0000
12:55725908:A:Tacceptor_gain1.0000
12:55725911:C:CTacceptor_gain1.0000
12:55725913:C:CTacceptor_gain1.0000
12:55725914:A:Tacceptor_gain1.0000
12:55726116:CCTA:Cdonor_loss1.0000
12:55726117:CTAC:Cdonor_loss1.0000
12:55726118:TACCT:Tdonor_loss1.0000
12:55726119:ACC:Adonor_loss1.0000

AlphaMissense

1565 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:55726226:C:AW154C0.999
12:55726226:C:GW154C0.999
12:55726179:C:GC170S0.993
12:55726180:A:TC170S0.993
12:55726228:A:GW154R0.993
12:55726228:A:TW154R0.993
12:55726182:C:GC169S0.991
12:55726183:A:TC169S0.991
12:55726251:C:GC146S0.990
12:55726252:A:TC146S0.990
12:55726248:C:TG147E0.989
12:55726249:C:AG147W0.989
12:55726254:C:GC145S0.987
12:55726255:A:TC145S0.987
12:55726181:G:CC169W0.986
12:55726182:C:TC169Y0.986
12:55726255:A:GC145R0.986
12:55726178:G:CC170W0.984
12:55726183:A:GC169R0.984
12:55726251:C:TC146Y0.984
12:55725830:C:GG212R0.983
12:55725830:C:TG212R0.983
12:55726158:C:GC177S0.983
12:55726159:A:TC177S0.983
12:55726227:C:GW154S0.983
12:55726248:C:AG147V0.983
12:55725892:C:GC191S0.982
12:55725893:A:TC191S0.982
12:55726250:A:CC146W0.980
12:55726253:G:CC145W0.980

dbSNP variants (sampled 300 via entrez): RS1000274649 (12:55727489 G>A,T), RS1000613765 (12:55730534 G>A,C), RS1000876538 (12:55729350 G>T), RS1000943290 (12:55730230 A>G), RS1001266481 (12:55729575 C>G,T), RS1001488475 (12:55726814 A>C,G), RS1001913268 (12:55724899 T>C), RS1001995245 (12:55725166 G>A,T), RS1002391724 (12:55728870 G>A,T), RS1002554272 (12:55731449 C>A,T), RS1002926676 (12:55726318 T>A,C), RS1003055261 (12:55725625 A>C), RS1003558165 (12:55725406 C>T), RS1004356209 (12:55729769 G>C,T), RS1004374956 (12:55728361 G>A)

Disease associations

OMIM: gene MIM:155740 | disease phenotypes: MIM:136880

GenCC curated gene-disease

Mondo (3): inherited retinal dystrophy (MONDO:0019118), fundus albipunctatus (MONDO:0007639), retinitis punctata albescens (MONDO:0018877)

Orphanet (3): OBSOLETE: Inherited retinal disorder (Orphanet:71862), Fundus albipunctatus (Orphanet:227796), Retinitis punctata albescens (Orphanet:52427)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0000556Retinal dystrophy

GWAS associations

3 associations (top):

StudyTraitp-value
GCST003219_5Advanced age-related macular degeneration4.000000e-09
GCST008310_10Cardiac Troponin-T levels3.000000e-07
GCST010002_217Refractive error6.000000e-174

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:1001492atrophic macular degeneration
EFO:0005043cardiac troponin T measurement

MeSH disease descriptors (2)

DescriptorNameTree numbers
D058499Retinal DystrophiesC11.768.585.658
C562733Fundus Albipunctatus (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3713303 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

2 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 405 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL3986824LANRAPLENIB2319
CHEMBL5083772BIIB-091286

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

Binding affinities (BindingDB)

11 measured of 11 human assays (11 total across all organisms); most potent 11 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
6-(6-amino-5-methylpyrazin-2-yl)-N-(4-(4-(oxetan-3-yl)piperazin-1-yl)phenyl)imidazo[1,2-a]pyrazin-8-amineIC506.2 nMUS-9504684: Syk inhibitors
2-(5-((6-(6-amino-5-methylpyrazin-2-yl)imidazo[1,2-a]pyrazin-8-yl)amino)-2-(4-(oxetan-3-yl)piperazin-1-yl)phenoxy)ethanolIC508.7 nMUS-9504684: Syk inhibitors
2-(5-((6-(6-aminopyrazin-2-yl)imidazo[1,2-a]pyrazin-8-yl)amino)-2-(4-(oxetan-3-yl)piperazin-1-yl)phenoxy)ethanolIC5012.2 nMUS-9504684: Syk inhibitors
(R)-(4-(4-((6-(6-aminopyrazin-2-yl)imidazo[1,2-a]pyrazin-8-yl)amino)phenyl)morpholin-2-yl)methanolIC5013.3 nMUS-9504684: Syk inhibitors
6-(6-aminopyrazin-2-yl)-N-(4-(4-(oxetan-3-yl)piperazin-1-yl)phenyl)imidazo[1,2-a]pyrazin-8-amineIC5013.5 nMUS-9504684: Syk inhibitors
2-((4-(4-((6-(6-aminopyrazin-2-yl)imidazo[1,2-a]pyrazin-8-yl)amino)phenyl)piperazin-1-yl)methyl)propane-1,3-diolIC5014.5 nMUS-9504684: Syk inhibitors
6-(5-amino-6-methyl-3-pyridinyl)-N-(4-morpholin-4-ylphenyl)imidazo[1,2-a]pyrazin-8-amineIC5016 nMUS-9504684: Syk inhibitors
6-(5-amino-3-pyridinyl)-N-(4-morpholin-4-ylphenyl)imidazo[1,2-a]pyrazin-8-amineIC5031 nMUS-9504684: Syk inhibitors
6-(6-aminopyrazin-2-yl)-5-methyl-N-(4-(4-(oxetan-3-yl)piperazin-1-yl)phenyl)imidazo[1,2-a]pyrazin-8-amineIC5044 nMUS-9504684: Syk inhibitors
6-(6-amino-3-pyridinyl)-N-(3,4-dimethoxyphenyl)imidazo[1,2-a]pyrazin-8-amineIC5053 nMUS-9504684: Syk inhibitors
6-(3-aminophenyl)-N-(3,4-dimethoxyphenyl)imidazo[1,2-a]pyrazin-8-amineIC50188 nMUS-9504684: Syk inhibitors

ChEMBL bioactivities

12 potent at pChembl≥5 of 14 total, top 12 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.48IC5033nMCHEMBL3953841
7.29IC5051nMCHEMBL3917084
7.10IC5080nMLANRAPLENIB
7.09IC5082nMBIIB-091
7.00IC50101nMCHEMBL3978560
6.92IC50120nMCHEMBL3902654
6.89IC50128nMCHEMBL3973635
6.80IC50157nMCHEMBL3929647
6.78IC50167nMCHEMBL3911668
6.60IC50250nMCHEMBL3952825
6.13IC50734nMCHEMBL3962740
6.09IC50809nMCHEMBL3981576

PubChem BioAssay actives

1 with measured affinity, of 3 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
1-tert-butyl-N-[(5R)-8-[2-[(1-methylpyrazol-4-yl)amino]pyrimidin-4-yl]-2-(oxetan-3-yl)-1,3,4,5-tetrahydro-2-benzazepin-5-yl]triazole-4-carboxamide1820597: Inhibition of CD63 (unknown origin) assessed as FcepsilonR induced basophil activationic500.0820uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, increases expression3
Tetrachlorodibenzodioxindecreases reaction, increases expression3
Particulate Matterdecreases expression, increases abundance, affects cotreatment, increases expression3
sodium arseniteaffects expression, increases expression2
N-Formylmethionine Leucyl-Phenylalanineincreases expression, increases reaction, affects reaction, decreases reaction2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Quercetinaffects reaction, increases expression2
Smokedecreases expression, increases expression2
Tobacco Smoke Pollutionincreases expression, affects expression2
Valproic Acidaffects cotreatment, increases expression2
Cyclosporineincreases expression2
bisphenol Fincreases expression1
fenebrutinibdecreases expression1
TAK-243increases sumoylation1
evobrutinibdecreases expression1
remibrutinibdecreases expression1
orelabrutinibdecreases expression1
rilzabrutinibdecreases expression1
triphenyl phosphateaffects expression1
titanium dioxideincreases expression1
beta-lapachoneincreases expression1
cupric chloridedecreases expression1
ceric oxideincreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation1
isobutyl alcoholaffects cotreatment, increases abundance, increases expression1
beta-methylcholineaffects expression1
yessotoxinincreases expression1
SB 203580decreases reaction, increases expression, increases reaction1
chloropicrindecreases expression1
K 7174increases expression1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3887150BindingHigh Throughput Syk Biochemical Assay: Syk activity was measured using KinEASE (Cisbio), a time-resolved fluorescence resonance energy transfer (TR-FRET) immunoassay. In this assay, Syk-catalyzes the phosphorylation of a XL665-labeled peptiSubstituted imidazo[1,2-a]pyrazines as Syk inhibitors

Cellosaurus cell lines

10 cell lines: 6 transformed cell line, 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A8RYCAP-CD63-tGFPTransformed cell line
CVCL_A8SACAP-CD63-tGFP-NullTransformed cell line
CVCL_A8SCCAP-CD63-tGFP-miRNA-493Transformed cell line
CVCL_A8SDCAP-CD63-tGFP-miRNA-744Transformed cell line
CVCL_B0ZKAbcam Hep-G2 CD63 KOCancer cell lineMale
CVCL_D7M7Ubigene A-549 CD63 KOCancer cell lineMale
CVCL_D9BIUbigene HEK293 CD63 KOTransformed cell lineFemale
CVCL_D9ZQUbigene HeLa CD63 KOCancer cell lineFemale
CVCL_SH90HAP1 CD63 (-)Cancer cell lineMale
CVCL_UF04HEK293 CD63 CRISPRTransformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04224207PHASE3COMPLETEDManagement of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855PHASE3NOT_YET_RECRUITINGA Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT03763227PHASE2COMPLETEDIntravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207PHASE2COMPLETEDMinocycline Treatment in Retinitis Pigmentosa
NCT04945772PHASE2COMPLETEDEfficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05902962PHASE1COMPLETEDSAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872PHASE1RECRUITINGThe Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826PHASE1COMPLETEDMAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)
NCT04855045PHASE2/PHASE3UNKNOWNAn Open-label, Dose Escalation and Double-masked, Randomized, Controlled Trial Evaluating Safety and Tolerability of Sepofarsen in Children (<8 Years of Age) With LCA10 Caused by Mutations in the CEP290 Gene.
NCT03872479PHASE1/PHASE2UNKNOWNSingle Ascending Dose Study in Participants With LCA10
NCT04123626PHASE1/PHASE2ACTIVE_NOT_RECRUITINGA Study to Evaluate the Safety and Tolerability of QR-1123 in Subjects With Autosomal Dominant Retinitis Pigmentosa Due to the P23H Mutation in the RHO Gene
NCT04545736PHASE1/PHASE2RECRUITINGOral Metformin for Treatment of ABCA4 Retinopathy
NCT06212297PHASE1/PHASE2ACTIVE_NOT_RECRUITINGFellow-eye Study (FE) of LX101 in Subjects With Inherited Retinal Dystrophy
NCT06852963PHASE1/PHASE2ACTIVE_NOT_RECRUITINGA Repeat-Dose, Open-Label, Two Arm Safety and Efficacy Study of Two Doses of VP-001 Administered Intravitreally in Participants With Confirmed PRPF31 Mutation-Associated Retinal Dystrophy, Including Participants Previously Treated With VP001
NCT07177196PHASE1/PHASE2ACTIVE_NOT_RECRUITINGPersonalized Antisense Oligonucleotide Therapy for a Single Participant With PRPH2 Mutation Associated With Retinal Dystrophy
NCT07063030EARLY_PHASE1RECRUITINGA Study of LX107 Gene Therapy in AIPL1-IRD Patients
NCT01546181Not specifiedCOMPLETEDRetinal Imaging by Adaptive Optics in Healthy Eyes and During Retinal and General Diseases
NCT01876147Not specifiedCOMPLETEDVisual and Functional Assessment in Low Vision Patients
NCT01920867Not specifiedUNKNOWNStem Cell Ophthalmology Treatment Study
NCT02014389Not specifiedRECRUITINGEvaluation of Objective Perimetry Using Chromatic Multifocal Pupillometer
NCT02983305Not specifiedCOMPLETEDOptical Head-Mounted Display Technology for Low Vision Rehabilitation
NCT03592017Not specifiedCOMPLETEDPerformance of Long-wavelength Autofluorescence Imaging
NCT03662386Not specifiedTERMINATEDProspective Analysis of Genotype-phenotype Correlations Observed in a Large Cohort of Patients With Hereditary Retinal Dystrophies - GEPHIRD
NCT03691168Not specifiedUNKNOWNMulti-center Observation of the Natural Course of Inherited Retinal Dystrophies
NCT03843840Not specifiedCOMPLETEDDual Wavelength OCT
NCT03853252Not specifiedCOMPLETEDiPS Cells of Patients for Models of Retinal Dystrophies
NCT05130385Not specifiedUNKNOWNHigh Resolution Optical Coherence Tomography
NCT05294978Not specifiedRECRUITINGEyeConic: Qualification for Cone-Optogenetics
NCT05573984Not specifiedACTIVE_NOT_RECRUITINGNatural History of PRPF31 Mutation-Associated Retinal Dystrophy
NCT05793515Not specifiedCOMPLETEDMechanisms of Inherited Retinal Dystrophies Using Whole Genome Sequencing and in Vitro and in Vivo Models
NCT05820100Not specifiedCOMPLETEDObservational Study to Assess the Reliability and Validity of the MLYMT and MLSDT
NCT05976139Not specifiedRECRUITINGMicropulsed Laser in Patients With Macular Oedema in Retinal Dystrophies
NCT06162585Not specifiedACTIVE_NOT_RECRUITINGNon-Interventional Long Term Follow-up Study of Participants Previously Enrolled in the RESTORE Study
NCT06177977Not specifiedRECRUITINGSS-HH-OCT as a Novel Diagnostic Modality for Early-Onset Retinal Dystrophies (EORDs)
NCT06375239Not specifiedRECRUITINGObservational Study to Assess Endpoint Operational Feasibility & Measurement Properties in Patients with Retinal Degeneration
NCT06908161Not specifiedNOT_YET_RECRUITINGFunctional Assessments in Vision Impairment
NCT07085533Not specifiedRECRUITINGNatural History Study of Inherited Retinal Diseases
NCT07502664Not specifiedRECRUITINGDevelopment and Evaluation of Functional Visual Field and Navigation Endpoints in Moderate to Profound Inherited Retinal Disease (DEFINE-IRD)
NCT07529041Not specifiedENROLLING_BY_INVITATIONReal-time Acoustic Biofeedback for Enhancing Fixation Stability: A Proof-of-concept Study to Improve Ophthalmic Imaging Diagnostic Quality
NCT02435940Not specifiedRECRUITINGInherited Retinal Degenerative Disease Registry