CLEC18B

Summary

CLEC18B (C-type lectin domain family 18 member B, HGNC:33849) is a protein-coding gene on chromosome 16q23.1, encoding C-type lectin domain family 18 member B (Q6UXF7). Binds polysaccharides in a Ca(2+)-independent manner.

Predicted to enable polysaccharide binding activity. Predicted to be located in Golgi apparatus; endosome; and sarcoplasmic reticulum. Predicted to be active in extracellular space.

Source: NCBI Gene 497190 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 81 total
• MANE Select transcript: NM_001385193

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33849
Approved symbol	CLEC18B
Name	C-type lectin domain family 18 member B
Location	16q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000140839
Ensembl biotype	protein_coding
OMIM	616572
Entrez	497190

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 retained_intron

ENST00000339953, ENST00000425714, ENST00000564842, ENST00000682950, ENST00000890001, ENST00000890002, ENST00000890003

RefSeq mRNA: 7 — MANE Select: NM_001385193 NM_001011880, NM_001385192, NM_001385193, NM_001385194, NM_001385195, NM_001421705, NM_001421759

CCDS: CCDS32484, CCDS92195

Canonical transcript exons

ENST00000682950 — 12 exons

Exon	Start	End
ENSE00002442531	74418059	74418298
ENSE00002464497	74409550	74409641
ENSE00002482599	74410905	74411034
ENSE00002485685	74411669	74411775
ENSE00002516396	74410536	74410632
ENSE00002582797	74408631	74409043
ENSE00003518759	74412154	74412246
ENSE00003549730	74413037	74413158
ENSE00003551188	74413579	74413676
ENSE00003681000	74420501	74420592
ENSE00003687435	74412773	74412880
ENSE00003919116	74421147	74421478

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 89.79.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adult mammalian kidney	UBERON:0000082	89.79	gold quality
kidney	UBERON:0002113	87.81	gold quality
cortex of kidney	UBERON:0001225	85.18	gold quality
right testis	UBERON:0004534	82.10	gold quality
left testis	UBERON:0004533	81.55	gold quality
testis	UBERON:0000473	80.46	gold quality
metanephros cortex	UBERON:0010533	79.04	gold quality
right hemisphere of cerebellum	UBERON:0014890	76.71	gold quality
cerebellar hemisphere	UBERON:0002245	76.52	gold quality
cerebellar cortex	UBERON:0002129	76.44	gold quality
cerebellum	UBERON:0002037	76.43	gold quality
lower esophagus mucosa	UBERON:0035834	75.69	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.14	gold quality
nucleus accumbens	UBERON:0001882	71.26	gold quality
tibial nerve	UBERON:0001323	71.20	gold quality
caudate nucleus	UBERON:0001873	70.70	gold quality
esophagus mucosa	UBERON:0002469	70.55	gold quality
cortical plate	UBERON:0005343	69.51	gold quality
left adrenal gland cortex	UBERON:0035825	69.27	gold quality
putamen	UBERON:0001874	69.10	gold quality
blood	UBERON:0000178	69.05	gold quality
substantia nigra	UBERON:0002038	68.65	gold quality
ascending aorta	UBERON:0001496	68.49	gold quality
amygdala	UBERON:0001876	68.26	gold quality
temporal lobe	UBERON:0001871	68.03	gold quality
thoracic aorta	UBERON:0001515	67.99	gold quality
hypothalamus	UBERON:0001898	67.87	gold quality
right frontal lobe	UBERON:0002810	67.31	gold quality
brain	UBERON:0000955	66.91	gold quality
Ammon’s horn	UBERON:0001954	66.91	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-114530	yes	593.93
E-GEOD-124472	yes	441.27
E-HCAD-10	yes	31.38
E-ANND-3	yes	2.77
E-CURD-135	no	360.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting CLEC18B, 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-4520-2-3P	99.14	69.28	1009
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-4329	97.68	66.26	1003
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-541-3P	96.07	66.11	1271
HSA-MIR-654-5P	96.07	66.18	1280
HSA-MIR-6821-3P	95.21	66.79	578
HSA-MIR-769-5P	94.45	64.56	603

Literature-anchored findings (GeneRIF, showing 2)

• The human C-type lectin 18 (clec18) gene cluster, which contains three clec18a, clec18b, and clec18c loci, is located in human chromosome 16q22. (PMID:26170455)
• The results from this study showed that CLEC18B was markedly elevated in both GBM tissues and cells, and exhibited strong inverse correlation with overall survival in GBM patients (PMID:29914265)

Cross-species orthologs

46 orthologs

Organism	Symbol	Gene ID
mus_musculus	Clec18a	ENSMUSG00000033633
rattus_norvegicus	Clec18a	ENSRNOG00000022721
drosophila_melanogaster	Ag5r	FBGN0015010
drosophila_melanogaster	Ag5r2	FBGN0020508
drosophila_melanogaster	CG9400	FBGN0030562
drosophila_melanogaster	CG10651	FBGN0032853
drosophila_melanogaster	CG9822	FBGN0034623
drosophila_melanogaster	CG17974	FBGN0034624
drosophila_melanogaster	CG3640	FBGN0035042
drosophila_melanogaster	CG8072	FBGN0036070
drosophila_melanogaster	CG6628	FBGN0036072
drosophila_melanogaster	scpr-C	FBGN0037879
drosophila_melanogaster	scpr-B	FBGN0037888
drosophila_melanogaster	scpr-A	FBGN0037889
drosophila_melanogaster	CG8483	FBGN0038126
drosophila_melanogaster	CG30486	FBGN0050486
drosophila_melanogaster	antr	FBGN0050488
drosophila_melanogaster	CG31286	FBGN0051286
drosophila_melanogaster	CG32313	FBGN0052313
drosophila_melanogaster	CG32679	FBGN0052679
drosophila_melanogaster	CG34002	FBGN0054002
drosophila_melanogaster	CG17575	FBGN0250842
drosophila_melanogaster	CG42564	FBGN0260766
drosophila_melanogaster	CG42780	FBGN0261848
drosophila_melanogaster	CG43775	FBGN0264297
drosophila_melanogaster	CG43776	FBGN0264298
drosophila_melanogaster	CG43777	FBGN0264299
caenorhabditis_elegans		WBGENE00004742
caenorhabditis_elegans		WBGENE00007397
caenorhabditis_elegans		WBGENE00008027
caenorhabditis_elegans		WBGENE00008028
caenorhabditis_elegans		WBGENE00008029
caenorhabditis_elegans		WBGENE00008030
caenorhabditis_elegans		WBGENE00008625
caenorhabditis_elegans		WBGENE00009891
caenorhabditis_elegans		WBGENE00009895
caenorhabditis_elegans		WBGENE00009896
caenorhabditis_elegans		WBGENE00012816
caenorhabditis_elegans		WBGENE00013971
caenorhabditis_elegans		WBGENE00013972
caenorhabditis_elegans		WBGENE00015246
caenorhabditis_elegans		WBGENE00017055
caenorhabditis_elegans		WBGENE00017183
caenorhabditis_elegans		WBGENE00019178
caenorhabditis_elegans		WBGENE00019179
caenorhabditis_elegans		WBGENE00021780

Paralogs (13): CRISP3 (ENSG00000096006), R3HDML (ENSG00000101074), CRISPLD2 (ENSG00000103196), CRISPLD1 (ENSG00000121005), GLIPR2 (ENSG00000122694), CRISP2 (ENSG00000124490), CRISP1 (ENSG00000124812), PI15 (ENSG00000137558), GLIPR1 (ENSG00000139278), CLEC18A (ENSG00000157322), CLEC18C (ENSG00000157335), GLIPR1L1 (ENSG00000173401), GLIPR1L2 (ENSG00000180481)

Protein

Protein identifiers

C-type lectin domain family 18 member B — Q6UXF7 (reviewed: Q6UXF7)

Alternative names: Mannose receptor-like protein 1

All UniProt accessions (2): Q6UXF7, A0A804HJ60

UniProt curated annotations — full annotation on UniProt →

Function. Binds polysaccharides in a Ca(2+)-independent manner.

Subcellular location. Secreted. Endoplasmic reticulum. Golgi apparatus. Endosome.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UXF7-1	1	yes
Q6UXF7-2	2

RefSeq proteins (7): NP_001011880, NP_001372121, NP_001372122, NP_001372123, NP_001372124, NP_001408634, NP_001408688 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000742	EGF	Domain
IPR001283	CRISP-related	Family
IPR001304	C-type_lectin-like	Domain
IPR014044	CAP_dom	Domain
IPR016186	C-type_lectin-like/link_sf	Homologous_superfamily
IPR016187	CTDL_fold	Homologous_superfamily
IPR018378	C-type_lectin_CS	Conserved_site
IPR035940	CAP_sf	Homologous_superfamily

Pfam: PF00059, PF00188

UniProt features (14 total): disulfide bond 4, splice variant 3, domain 3, signal peptide 1, chain 1, sequence conflict 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXF7-F1	79.28	0.40

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 (4): 236–249, 251–260, 327–441, 417–433

Glycosylation sites (1): 144

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): GOCC_SARCOPLASM, GOMF_POLYSACCHARIDE_BINDING, chr16q23, BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_UP, MEBARKI_HCC_PROGENITOR_FZD8CRD_DN, DESCARTES_MAIN_FETAL_METANEPHRIC_CELLS, DESCARTES_FETAL_EYE_ASTROCYTES, DESCARTES_FETAL_KIDNEY_METANEPHRIC_CELLS, ARID3B_TARGET_GENES, GOCC_ENDOSOME, NABA_ECM_AFFILIATED, NABA_MATRISOME_ASSOCIATED, NABA_MATRISOME, GOCC_GOLGI_APPARATUS, GOMF_CARBOHYDRATE_BINDING

GO Biological Process (0):

GO Molecular Function (2): polysaccharide binding (GO:0030247), carbohydrate binding (GO:0030246)

GO Cellular Component (6): obsolete extracellular space (GO:0005615), endosome (GO:0005768), Golgi apparatus (GO:0005794), sarcoplasmic reticulum (GO:0016529), extracellular region (GO:0005576), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
endomembrane system	3
cytoplasm	2
intracellular membrane-bounded organelle	2
carbohydrate binding	1
binding	1
cytoplasmic vesicle	1
endoplasmic reticulum	1
sarcoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

180 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC18B	ARL14EPL	P0DKL9	575
CLEC18B	OR4F17	Q8NGA8	473
CLEC18B	OR4F5	Q8NH21	448
CLEC18B	ANTKMT	Q9BQD7	381
CLEC18B	TMEM52B	Q4KMG9	370
CLEC18B	PAIP2B	Q9ULR5	348
CLEC18B	TMEM72	A0PK05	331
CLEC18B	CEP76	Q8TAP6	303
CLEC18B	COG4	Q9H9E3	295
CLEC18B	L3MBTL4	Q8NA19	290
CLEC18B	RNF152	Q8N8N0	248
CLEC18B	IFT38	Q96AJ1	248
CLEC18B	MYL12B	O14950	247
CLEC18B	BMS1	Q14692	247
CLEC18B	PPP4R1	Q8TF05	247

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A5D8T8, O35217, O75078, O75882, O75900, O88272, O88507, O88676, O95633, P08887, P0C7M8, P0C7M9, P26992, P78539, Q00961, Q01098, Q08406, Q0ZCA7, Q14957, Q1LZB9, Q2TBM7, Q4V7F2, Q5EA46, Q5VV63, Q63769, Q642A6, Q6A051, Q6IA17, Q6P1D5, Q6PCB0, Q6UXF7, Q71DR4, Q7TNS7, Q7TSQ1, Q8NCF0, Q8R2Z5, Q8R366, Q91XD7, Q96FT7, Q96HD1

Diamond homologs: A0A218QX58, A1BQQ5, A5D8T8, A6YPK1, A8S6B6, B0VXV6, B2MVK7, B7FDI0, B7FDI1, C0ITL3, D4P2Y4, D8VNS1, F7C0L1, F8J2D4, G3CJR9, O19010, P0DMB9, P0DMT4, P0DPU0, P0DSI3, P10736, P10737, P11670, P16562, P16563, P35759, P35778, P35779, P35780, P35781, P35782, P35783, P35785, P35786, P35787, P36110, P47032, P54108, P60623, P79845

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	12
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2098 predictions. Top by Δscore:

Variant	Effect	Δscore
16:74409549:CCAAA:C	donor_gain	1.0000
16:74409637:CAAAC:C	acceptor_gain	1.0000
16:74409641:CCT:C	acceptor_loss	1.0000
16:74409643:T:A	acceptor_loss	1.0000
16:74409650:CAGGG:C	acceptor_gain	1.0000
16:74409651:A:T	acceptor_gain	1.0000
16:74409664:C:CT	acceptor_gain	1.0000
16:74410530:ACTT:A	donor_loss	1.0000
16:74410531:CTTA:C	donor_loss	1.0000
16:74410532:TTAC:T	donor_loss	1.0000
16:74410533:TACCC:T	donor_loss	1.0000
16:74410534:A:AC	donor_gain	1.0000
16:74410534:AC:A	donor_gain	1.0000
16:74410534:ACC:A	donor_gain	1.0000
16:74410535:C:CC	donor_gain	1.0000
16:74410535:CC:C	donor_gain	1.0000
16:74410535:CCC:C	donor_gain	1.0000
16:74410535:CCCGT:C	donor_gain	1.0000
16:74410639:C:CT	acceptor_gain	1.0000
16:74410639:C:T	acceptor_gain	1.0000
16:74410969:C:CT	acceptor_gain	1.0000
16:74420495:ACTC:A	donor_loss	1.0000
16:74420496:CTCA:C	donor_loss	1.0000
16:74420497:TCACC:T	donor_loss	1.0000
16:74420498:CA:C	donor_loss	1.0000
16:74420499:A:AC	donor_gain	1.0000
16:74420499:ACCAG:A	donor_gain	1.0000
16:74420500:C:CC	donor_gain	1.0000
16:74420500:C:CT	donor_loss	1.0000
16:74420500:CCAGC:C	donor_gain	1.0000

AlphaMissense

2924 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:74409596:C:A	W428C	0.994
16:74409596:C:G	W428C	0.994
16:74413102:C:G	C204S	0.991
16:74413103:A:T	C204S	0.991
16:74413039:C:G	C225S	0.990
16:74413040:A:T	C225S	0.990
16:74409582:C:G	C433S	0.989
16:74409583:A:T	C433S	0.989
16:74410562:A:C	F395L	0.988
16:74410562:A:T	F395L	0.988
16:74410564:A:G	F395L	0.988
16:74411673:C:G	C327S	0.988
16:74411674:A:T	C327S	0.988
16:74412862:C:G	C232S	0.988
16:74412863:A:T	C232S	0.988
16:74413092:G:C	C207W	0.988
16:74413093:C:T	C207Y	0.988
16:74410909:C:A	W370C	0.987
16:74410909:C:G	W370C	0.987
16:74413039:C:T	C225Y	0.987
16:74413093:C:G	C207S	0.987
16:74413094:A:T	C207S	0.987
16:74413101:A:C	C204W	0.987
16:74412778:C:T	C260Y	0.985
16:74413103:A:G	C204R	0.985
16:74412850:C:G	C236S	0.984
16:74412850:C:T	C236Y	0.984
16:74412851:A:T	C236S	0.984
16:74413094:A:G	C207R	0.984
16:74409558:C:G	C441S	0.983

dbSNP variants (sampled 300 via entrez): RS1000262178 (16:74422771 C>T), RS1000314176 (16:74423861 T>C), RS1000599627 (16:74418693 T>C,G), RS1000650571 (16:74419332 G>A), RS1001586666 (16:74425212 A>G), RS1001931196 (16:74424641 A>AG), RS1002323828 (16:74421565 G>A), RS1003877642 (16:74422315 A>T), RS1004495474 (16:74421697 C>G,T), RS1004834207 (16:74416927 A>G), RS1005448725 (16:74424773 A>G), RS1010255413 (16:74424062 G>A), RS1011895187 (16:74417724 T>G), RS1012346061 (16:74414565 A>G), RS1012704803 (16:74409657 T>C)

Disease associations

OMIM: gene MIM:616572 | 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
GCST008758_70	Pre-treatment viral load in HIV-1 infection	8.000000e-18

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010125	viral load

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Enzyme Inhibitors	increases O-linked glycosylation, decreases activity	1
Indomethacin	affects cotreatment, decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
Aflatoxin B1	decreases expression	1
Copper Sulfate	decreases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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