CD302

Summary

CD302 (CD302 molecule, HGNC:30843) is a protein-coding gene on chromosome 2q24.2, encoding CD302 antigen (Q8IX05). Multifunctional C-type lectin receptor involved in endocytosis, phagocytosis and regulation of cell adhesion and migration.

CD302 is a C-type lectin receptor involved in cell adhesion and migration, as well as endocytosis and phagocytosis (Kato et al., 2007 [PubMed 17947679]).

Source: NCBI Gene 9936 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_014880

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30843
Approved symbol	CD302
Name	CD302 molecule
Location	2q24.2
Locus type	gene with protein product
Status	Approved
Aliases	DCL-1, KIAA0022, BIMLEC, CLEC13A
Ensembl gene	ENSG00000241399
Ensembl biotype	protein_coding
OMIM	612246
Entrez	9936

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000259053, ENST00000429078, ENST00000480212, ENST00000553424, ENST00000856855, ENST00000856856, ENST00000856857, ENST00000856858, ENST00000856859, ENST00000856860, ENST00000856861, ENST00000966882, ENST00000966883

RefSeq mRNA: 3 — MANE Select: NM_014880 NM_001198763, NM_001198764, NM_014880

CCDS: CCDS33308, CCDS56139, CCDS74595

Canonical transcript exons

ENST00000259053 — 6 exons

Exon	Start	End
ENSE00003482872	159783359	159783469
ENSE00003560104	159768628	159772053
ENSE00003657339	159798132	159798208
ENSE00003730131	159777938	159777964
ENSE00003735029	159780005	159780178
ENSE00003743188	159780882	159780998

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 97.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.8494 / max 627.3352, expressed in 1477 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
31454	18.7221	1411
31455	4.9253	1131
31456	0.2020	85

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower lobe of lung	UBERON:0008949	97.76	gold quality
monocyte	CL:0000576	97.72	gold quality
mononuclear cell	CL:0000842	97.71	gold quality
leukocyte	CL:0000738	97.35	gold quality
right lung	UBERON:0002167	97.02	gold quality
liver	UBERON:0002107	96.54	gold quality
synovial joint	UBERON:0002217	96.24	gold quality
trabecular bone tissue	UBERON:0002483	96.21	gold quality
layer of synovial tissue	UBERON:0007616	95.57	gold quality
right lobe of liver	UBERON:0001114	95.37	gold quality
calcaneal tendon	UBERON:0003701	95.34	gold quality
superficial temporal artery	UBERON:0001614	95.31	gold quality
urethra	UBERON:0000057	95.22	gold quality
mammary duct	UBERON:0001765	94.99	gold quality
skin of hip	UBERON:0001554	94.80	gold quality
right coronary artery	UBERON:0001625	94.20	gold quality
decidua	UBERON:0002450	93.98	gold quality
pericardium	UBERON:0002407	93.95	gold quality
epithelium of mammary gland	UBERON:0003244	93.88	gold quality
jejunal mucosa	UBERON:0000399	93.65	gold quality
lung	UBERON:0002048	93.53	gold quality
pigmented layer of retina	UBERON:0001782	93.52	gold quality
blood vessel layer	UBERON:0004797	93.46	gold quality
thoracic mammary gland	UBERON:0005200	93.44	gold quality
pleura	UBERON:0000977	93.32	gold quality
mammary gland	UBERON:0001911	93.24	gold quality
parietal pleura	UBERON:0002400	93.24	gold quality
visceral pleura	UBERON:0002401	93.24	gold quality
adipose tissue	UBERON:0001013	93.08	gold quality
gall bladder	UBERON:0002110	93.06	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-CURD-46	yes	33.68
E-MTAB-9221	yes	28.53
E-GEOD-134144	yes	26.30
E-HCAD-10	yes	26.04
E-CURD-112	yes	24.96
E-CURD-88	yes	20.61
E-ANND-3	yes	14.37
E-MTAB-9467	yes	11.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

149 targeting CD302, 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-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548N	99.98	71.94	4170

Literature-anchored findings (GeneRIF, showing 6)

• Hodgkin’s lymphoma cell lines express a fusion protein encoded by intergenically spliced mRNA for the multilectin receptor DEC-205 (CD205) and a novel C-type lectin receptor DCL-1 (PMID:12824192)
• hDCL-1 is an unconventional lectin receptor that plays roles not only in endocytosis/phagocytosis but also in cell adhesion and migration (PMID:17947679)
• DLC1 equilibrium unfolding is characterized at the amino acid level. (PMID:19317456)
• These studies confirm a functional role for CD302 in myeloid dendritic cells migration. (PMID:27316686)
• Particle Morphology of Medusavirus Inside and Outside the Cells Reveals a New Maturation Process of Giant Viruses. (PMID:35297671)
• The Human Liver-Expressed Lectin CD302 Restricts Hepatitis C Virus Infection. (PMID:35297672)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cd302	ENSDARG00000086100
mus_musculus	Cd302	ENSMUSG00000060703
rattus_norvegicus	Cd302	ENSRNOG00000006623
caenorhabditis_elegans		WBGENE00010228

Paralogs (4): MRC2 (ENSG00000011028), LY75 (ENSG00000054219), PLA2R1 (ENSG00000153246), MRC1 (ENSG00000260314)

Protein

Protein identifiers

CD302 antigen — Q8IX05 (reviewed: Q8IX05)

Alternative names: C-type lectin BIMLEC, C-type lectin domain family 13 member A, DEC205-associated C-type lectin 1, Type I transmembrane C-type lectin receptor DCL-1

All UniProt accessions (2): Q8IX05, A0A087WT00

UniProt curated annotations — full annotation on UniProt →

Function. Multifunctional C-type lectin receptor involved in endocytosis, phagocytosis and regulation of cell adhesion and migration. Plays a critical role in guiding dendritic cells to lymph nodes. Also functions as a restriction factor for Hepatitis C virus (HCV) at the liver cell surface, likely by inhibiting a viral cell entry step.

Subcellular location. Cell membrane. Cell projection. Filopodium. Cytoplasm. Cell cortex. Microvillus.

Tissue specificity. Expressed at moderate levels in monocytes, myeloid blood dendritic cells and granulocytes and at low levels in plasmacytoid blood dendritic cells, monocyte-derived macrophages and monocyte-derived dendritic cells, with no expression detected in T-lymphocytes, B-lymphocytes and natural killer cells (at protein level). Expressed widely in different tissues, with highest expression levels in liver, lung, peripheral blood leukocytes and spleen, and lowest levels in neuronal tissues, skeletal muscle and ovary. Isoform 2 and isoform 3 are expressed in malignant Hodgkin lymphoma cells called Hodgkin and Reed-Sternberg (HRS) cells.

Post-translational modifications. May be heterogeneously N-glycosylated in some cell types.

Miscellaneous. Isoform 2 and isoform 3 are produced in HRS cells by a transcriptional control mechanism which cotranscribe an mRNA containing LY75 and CD302 prior to generating the intergenically spliced mRNA to produce LY75/CD302 fusion proteins. Produced by intergenic splicing of LY75 and CD302.

Isoforms (5)

UniProt ID	Names	Canonical?
Q8IX05-1	1	yes
O60449-1	4
Q8IX05-2	5
O60449-2	2, Fusion protein variant V34-2
O60449-3	3, Fusion protein variant V33-2

RefSeq proteins (3): NP_001185692, NP_001185693, NP_055695* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001304	C-type_lectin-like	Domain
IPR016186	C-type_lectin-like/link_sf	Homologous_superfamily
IPR016187	CTDL_fold	Homologous_superfamily
IPR050111	C-type_lectin/snaclec_domain	Family

Pfam: PF00059

UniProt features (25 total): strand 8, turn 3, helix 2, topological domain 2, splice variant 2, signal peptide 1, chain 1, sequence variant 1, sequence conflict 1, transmembrane region 1, domain 1, glycosylation site 1, disulfide bond 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2NAN	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IX05-F1	80.53	0.50

Functional residue map

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

Disulfide bonds (1): 128–143

Glycosylation sites (1): 109

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 215 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, MODULE_45, GOBP_VESICLE_MEDIATED_TRANSPORT, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, GNF2_MCL1, GNF2_CD1D, KOYAMA_SEMA3B_TARGETS_UP, HOSHIDA_LIVER_CANCER_SUBCLASS_S3, chr2q24, SANSOM_APC_TARGETS_DN, GNF2_HCK, BASAKI_YBX1_TARGETS_DN, VECCHI_GASTRIC_CANCER_EARLY_DN, GOBP_IMPORT_INTO_CELL, RIGGINS_TAMOXIFEN_RESISTANCE_DN

GO Biological Process (1): phagocytosis (GO:0006909)

GO Molecular Function (3): carbohydrate binding (GO:0030246), signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (6): microvillus (GO:0005902), cell cortex (GO:0005938), membrane (GO:0016020), filopodium (GO:0030175), cytoplasm (GO:0005737), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
binding	2
actin-based cell projection	2
endocytosis	1
molecular transducer activity	1
actin filament bundle	1
cytoplasm	1
cell periphery	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

612 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD302	AGO1	Q9UL18	785
CD302	DICER1	Q9UPY3	723
CD302	SRRT	Q9BXP5	670
CD302	MILR1	Q7Z6M3	571
CD302	DROSHA	Q9NRR4	546
CD302	PIWIL4	Q7Z3Z4	512
CD302	AGO4	Q9HCK5	510
CD302	PIWIL1	Q96J94	507
CD302	LY75	O60449	500
CD302	SNRPD3	P43331	443
CD302	AGO2	Q9UKV8	409
CD302	CX3CL1	P78423	408
CD302	HSPB8	Q9UJY1	392
CD302	SLC27A3	Q5K4L6	384
CD302	SEC14L2	O76054	379

IntAct

33 interactions, top by confidence:

A	B	Type	Score
CD302	IL7R	psi-mi:“MI:0915”(physical association)	0.560
CD302	IL10RA	psi-mi:“MI:0915”(physical association)	0.560
CD302	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
CD302	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
IL7R	CD302	psi-mi:“MI:0915”(physical association)	0.560
IL10RA	CD302	psi-mi:“MI:0915”(physical association)	0.560
CD53	CD302	psi-mi:“MI:0915”(physical association)	0.560
OPRM1	CD302	psi-mi:“MI:0915”(physical association)	0.560
IFNGR2	CD302	psi-mi:“MI:0915”(physical association)	0.560
CD302	GPX8	psi-mi:“MI:0915”(physical association)	0.560
GET1	CD302	psi-mi:“MI:0915”(physical association)	0.560
ARL13B	CD302	psi-mi:“MI:0915”(physical association)	0.560
METTL3	TUBAL3	psi-mi:“MI:0914”(association)	0.350
	FAM171A2	psi-mi:“MI:0914”(association)	0.350
CD302	ERGIC3	psi-mi:“MI:0915”(physical association)	0.000
CD302	CD53	psi-mi:“MI:0915”(physical association)	0.000
CD302	OPRM1	psi-mi:“MI:0915”(physical association)	0.000
CD302	IFNGR2	psi-mi:“MI:0915”(physical association)	0.000
CD302	GPX8	psi-mi:“MI:0915”(physical association)	0.000
CD302	ARL13B	psi-mi:“MI:0915”(physical association)	0.000
CD302	GET1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): FATE1 (Two-hybrid), CD302 (Affinity Capture-MS), CD302 (Two-hybrid), CD302 (Two-hybrid), CD302 (Two-hybrid), CD302 (Two-hybrid), CD302 (Two-hybrid), CD302 (Two-hybrid), CD302 (Two-hybrid), CD302 (Affinity Capture-MS), CD302 (Affinity Capture-MS), CD302 (Affinity Capture-Western)

ESM2 similar proteins: A0A7H0DND3, A1XRN2, A8WH72, A8WH74, A8WH75, A8WUV1, B1A4M7, B1A4N2, B1A4N8, B1A4P2, B1A4P6, B1A4P7, B1A4P8, B1A4P9, B1A4Q0, B1A4Q2, B1A4Q3, B1A4Q5, B1A4Q6, B1A4Q8, B1A4Q9, B1A4R0, B1A4R4, B2D1Y0, O55159, P0DQP8, P10721, P16234, P21057, P21755, P21756, P24761, P24765, P26618, P26619, P33851, Q16YE7, Q1L867, Q3T0L5, Q5FVR3

Diamond homologs: A8WH72, A8WH74, A8WH75, Q02988, Q5FVR3, Q8IX05, Q9DCG2, O45824, P49260, Q60767, Q91ZX1, Q9PSM5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

10 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

846 predictions. Top by Δscore:

Variant	Effect	Δscore
2:159777933:CTTA:C	donor_loss	1.0000
2:159777934:TTA:T	donor_loss	1.0000
2:159777935:TA:T	donor_loss	1.0000
2:159777936:A:T	donor_loss	1.0000
2:159777937:C:CG	donor_loss	1.0000
2:159777961:GGGA:G	acceptor_gain	1.0000
2:159777965:C:CC	acceptor_gain	1.0000
2:159779999:ACTT:A	donor_loss	1.0000
2:159780001:TT:T	donor_loss	1.0000
2:159780001:TTA:T	donor_loss	1.0000
2:159780002:TA:T	donor_loss	1.0000
2:159780003:A:AC	donor_gain	1.0000
2:159780003:A:T	donor_loss	1.0000
2:159780003:ACTAG:A	donor_gain	1.0000
2:159780004:C:CA	donor_loss	1.0000
2:159780004:C:CC	donor_gain	1.0000
2:159780004:CT:C	donor_gain	1.0000
2:159780004:CTA:C	donor_gain	1.0000
2:159780004:CTAG:C	donor_gain	1.0000
2:159780004:CTAGC:C	donor_gain	1.0000
2:159780878:TTA:T	donor_loss	1.0000
2:159780879:TA:T	donor_loss	1.0000
2:159780880:A:AC	donor_gain	1.0000
2:159780880:A:T	donor_loss	1.0000
2:159780880:AC:A	donor_gain	1.0000
2:159780880:ACCAT:A	donor_gain	1.0000
2:159780881:C:CC	donor_gain	1.0000
2:159780881:C:CG	donor_loss	1.0000
2:159780881:C:CT	donor_loss	1.0000
2:159780881:CC:C	donor_gain	1.0000

AlphaMissense

1538 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:159780060:C:A	W138C	0.998
2:159780060:C:G	W138C	0.998
2:159780162:C:A	W104C	0.997
2:159780162:C:G	W104C	0.997
2:159780062:A:G	W138R	0.996
2:159780062:A:T	W138R	0.996
2:159780016:C:G	C153S	0.993
2:159780017:A:T	C153S	0.993
2:159780164:A:G	W104R	0.993
2:159780164:A:T	W104R	0.993
2:159783370:C:G	C56S	0.992
2:159783371:A:T	C56S	0.992
2:159783371:A:G	C56R	0.988
2:159780129:C:A	W115C	0.987
2:159780129:C:G	W115C	0.987
2:159780980:A:T	I66K	0.987
2:159783369:A:C	C56W	0.986
2:159780017:A:G	C153R	0.985
2:159780015:G:C	C153W	0.984
2:159780016:C:T	C153Y	0.982
2:159780061:C:G	W138S	0.982
2:159780092:A:G	C128R	0.982
2:159780046:C:G	C143S	0.981
2:159780047:A:T	C143S	0.981
2:159780091:C:G	C128S	0.979
2:159780092:A:T	C128S	0.979
2:159780980:A:C	I66R	0.979
2:159780982:G:C	S65R	0.979
2:159780982:G:T	S65R	0.979
2:159780984:T:G	S65R	0.979

dbSNP variants (sampled 300 via entrez): RS1000026673 (2:159789003 T>C), RS1000071193 (2:159777069 T>C,G), RS1000242066 (2:159775900 T>G), RS1000250223 (2:159782567 TACAA>T), RS1000352494 (2:159769754 C>T), RS1000403869 (2:159782440 G>A,C,T), RS1000549648 (2:159795222 CG>C,CGG), RS1000561141 (2:159784013 A>G), RS1000579684 (2:159777137 G>A,C), RS1000655401 (2:159787903 G>C), RS1000822467 (2:159771409 A>G), RS1000891579 (2:159769955 T>C,G), RS1000962225 (2:159775736 C>A), RS1001046313 (2:159795686 A>C), RS1001086571 (2:159771038 A>C)

Disease associations

OMIM: gene MIM:612246 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST007277_3	Tourette syndrome	2.000000e-07
GCST009391_1633	Metabolite levels	9.000000e-07
GCST012490_496	Femur bone mineral density x serum urate levels interaction	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007787	plasma betaine measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	9
bisphenol A	increases expression, affects cotreatment	2
Dexamethasone	increases expression, affects cotreatment	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
quercitrin	decreases expression	1
terbufos	increases methylation	1
trichostatin A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
monomethylarsonous acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
Dasatinib	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	decreases expression	1
Bilirubin	decreases expression	1
Cadmium	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1

Clinical trials (associated diseases)

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