CLEC18C

Summary

CLEC18C (C-type lectin domain family 18 member C, HGNC:28538) is a protein-coding gene on chromosome 16q22.1, encoding C-type lectin domain family 18 member C (Q8NCF0). Binds polysaccharidesin a Ca(2+)-independent manner with a preferentially binding to fucoidan, beta-glucans and galactans.

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

Source: NCBI Gene 283971 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_173619

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28538
Approved symbol	CLEC18C
Name	C-type lectin domain family 18 member C
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC34761
Ensembl gene	ENSG00000157335
Ensembl biotype	protein_coding
OMIM	616573
Entrez	283971

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000314151, ENST00000536907, ENST00000541793, ENST00000561612, ENST00000562923, ENST00000564976, ENST00000565806, ENST00000569201, ENST00000569268, ENST00000569347, ENST00000618957, ENST00000861289

RefSeq mRNA: 2 — MANE Select: NM_173619 NM_001421706, NM_173619

CCDS: CCDS32473

Canonical transcript exons

ENST00000541793 — 13 exons

Exon	Start	End
ENSE00002479181	70183753	70183859
ENSE00002479726	70173787	70173951
ENSE00002507605	70184494	70184623
ENSE00002508090	70174173	70174402
ENSE00002523374	70184896	70184992
ENSE00003496115	70185885	70185976
ENSE00003497132	70182647	70182754
ENSE00003506663	70183281	70183373
ENSE00003544874	70174947	70175038
ENSE00003600090	70182368	70182489
ENSE00003612265	70181850	70181947
ENSE00003664389	70177241	70177480
ENSE00003689987	70186483	70186895

Expression profiles

Bgee: expression breadth ubiquitous, 120 present calls, max score 83.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0095 / max 14.9797, expressed in 2 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154868	0.0095	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adult mammalian kidney	UBERON:0000082	83.13	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.77	gold quality
kidney	UBERON:0002113	78.19	gold quality
cortex of kidney	UBERON:0001225	70.16	gold quality
right testis	UBERON:0004534	69.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	69.26	gold quality
left testis	UBERON:0004533	69.05	gold quality
testis	UBERON:0000473	68.52	gold quality
blood	UBERON:0000178	64.73	gold quality
metanephros cortex	UBERON:0010533	64.32	gold quality
ascending aorta	UBERON:0001496	61.53	gold quality
thoracic aorta	UBERON:0001515	60.87	gold quality
cerebellar hemisphere	UBERON:0002245	59.63	gold quality
right hemisphere of cerebellum	UBERON:0014890	59.56	gold quality
cerebellum	UBERON:0002037	59.46	gold quality
cerebellar cortex	UBERON:0002129	59.30	gold quality
mucosa of transverse colon	UBERON:0004991	59.21	gold quality
bone marrow cell	CL:0002092	57.12	gold quality
ventricular zone	UBERON:0003053	56.16	gold quality
descending thoracic aorta	UBERON:0002345	55.58	gold quality
duodenum	UBERON:0002114	55.30	gold quality
right coronary artery	UBERON:0001625	55.02	gold quality
left adrenal gland cortex	UBERON:0035825	54.40	gold quality
nucleus accumbens	UBERON:0001882	53.92	gold quality
putamen	UBERON:0001874	53.85	gold quality
cortical plate	UBERON:0005343	53.45	gold quality
tibial nerve	UBERON:0001323	53.24	gold quality
caudate nucleus	UBERON:0001873	52.72	gold quality
colonic epithelium	UBERON:0000397	52.54	gold quality
right uterine tube	UBERON:0001302	52.08	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting CLEC18C, 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-4776-3P	100.00	68.73	1340
HSA-MIR-4520-2-3P	99.14	69.28	1009
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-10A-5P	98.89	69.85	712
HSA-MIR-10B-5P	98.89	69.86	711
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-6821-3P	95.21	66.79	578
HSA-MIR-1228-5P	93.60	63.91	91

Literature-anchored findings (GeneRIF, showing 1)

• 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)

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), CLEC18B (ENSG00000140839), CLEC18A (ENSG00000157322), GLIPR1L1 (ENSG00000173401), GLIPR1L2 (ENSG00000180481)

Protein

Protein identifiers

C-type lectin domain family 18 member C — Q8NCF0 (reviewed: Q8NCF0)

Alternative names: Mannose receptor-like protein 3

All UniProt accessions (4): Q8NCF0, F5H550, H3BSF2, H3BUD1

UniProt curated annotations — full annotation on UniProt →

Function. Binds polysaccharidesin a Ca(2+)-independent manner with a preferentially binding to fucoidan, beta-glucans and galactans.

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

Tissue specificity. Detected in peripheral blood cells.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NCF0-1	1	yes
Q8NCF0-2	2

RefSeq proteins (2): NP_001408635, NP_775890* (*=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 (15 total): disulfide bond 4, sequence conflict 3, domain 3, splice variant 2, signal peptide 1, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NCF0-F1	82.39	0.56

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, 327–432, 408–424

Glycosylation sites (1): 144

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): MORF_MBD4, chr16q22, MORF_RAB5A, GCM_NPM1, MORF_PSMC2, GCM_PSME1, SRF_C, GATA6_01, AACTTT_UNKNOWN, CCCNNGGGAR_OLF1_01, WGGAATGY_TEF1_Q6, SCGGAAGY_ELK1_02, MORF_PRKAR1A, ELK1_02, MORF_PSMC1

GO Biological Process (0):

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

GO Cellular Component (5): obsolete extracellular space (GO:0005615), endosome (GO:0005768), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), extracellular region (GO:0005576)

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
cellular anatomical structure	1

Protein interactions and networks

STRING

118 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC18C	C1QTNF9B	B2RNN3	505
CLEC18C	TSKU	Q8WUA8	351
CLEC18C	COG4	Q9H9E3	350
CLEC18C	LGI4	Q8N135	348
CLEC18C	EPDR1	Q9UM22	347
CLEC18C	TPSG1	Q9NRR2	326
CLEC18C	CREG1	O75629	315
CLEC18C	COXFA4L3	Q9C002	310
CLEC18C	MRRF	Q96E11	295
CLEC18C	ZG16	O60844	288
CLEC18C	RTL4	Q6ZR62	274
CLEC18C	ADAMTS8	Q9UP79	256
CLEC18C	HABP2	Q14520	254
CLEC18C	RGCC	Q9H4X1	240
CLEC18C	TMEM37	Q8WXS4	224

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CLEC18C	NFKBIL1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (1): NFKBIL1 (Two-hybrid)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2164 predictions. Top by Δscore:

Variant	Effect	Δscore
16:70174945:A:AG	acceptor_gain	1.0000
16:70174946:G:GT	acceptor_gain	1.0000
16:70174946:GC:G	acceptor_gain	1.0000
16:70174946:GCCCT:G	acceptor_gain	1.0000
16:70175034:GGCTG:G	donor_gain	1.0000
16:70175035:GCTG:G	donor_gain	1.0000
16:70175035:GCTGG:G	donor_gain	1.0000
16:70175037:TGG:T	donor_loss	1.0000
16:70175038:GGTG:G	donor_loss	1.0000
16:70175039:G:GG	donor_gain	1.0000
16:70175039:GTG:G	donor_loss	1.0000
16:70175040:T:G	donor_loss	1.0000
16:70175041:GA:G	donor_loss	1.0000
16:70175042:AGTA:A	donor_loss	1.0000
16:70184558:T:TA	acceptor_gain	1.0000
16:70184989:ACGGG:A	donor_loss	1.0000
16:70184990:CGG:C	donor_gain	1.0000
16:70184990:CGGG:C	donor_loss	1.0000
16:70184991:GG:G	donor_gain	1.0000
16:70184991:GGG:G	donor_gain	1.0000
16:70184991:GGGTA:G	donor_loss	1.0000
16:70184992:GG:G	donor_gain	1.0000
16:70184993:GTAA:G	donor_loss	1.0000
16:70184994:T:A	donor_loss	1.0000
16:70185861:T:TA	acceptor_gain	1.0000
16:70185871:ACCAT:A	acceptor_gain	1.0000
16:70185874:AT:A	acceptor_gain	1.0000
16:70185875:T:G	acceptor_gain	1.0000
16:70185875:T:TA	acceptor_gain	1.0000
16:70185882:CAGGT:C	acceptor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000160589 (16:70179853 C>T), RS1001104830 (16:70174382 A>G), RS1001601065 (16:70176346 G>A,C), RS1001651639 (16:70177665 G>GT), RS1002605456 (16:70173653 G>A), RS1004106975 (16:70172772 C>T), RS1004564820 (16:70173576 G>A), RS1005963982 (16:70186090 C>T), RS1006014863 (16:70186586 T>A), RS1007457352 (16:70179958 T>C), RS1007819169 (16:70178885 C>G,T), RS1008411889 (16:70174439 C>G,T), RS1008879290 (16:70175410 G>A,T), RS1009912327 (16:70173962 G>A,T), RS1014324159 (16:70178771 T>G)

Disease associations

OMIM: gene MIM:616573 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST010703_100	Brain morphology (MOSTest)	2.000000e-40
GCST011011_63	Youthful appearance (self-reported)	5.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ethyl-p-hydroxybenzoate	decreases expression	1
hydroxyhydroquinone	decreases expression	1
Air Pollutants	increases abundance, affects expression	1
Benzo(a)pyrene	decreases methylation	1
Ozone	affects expression, increases abundance	1
Smoke	increases expression	1
Valproic Acid	increases methylation	1
Gold Compounds	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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