CLEC17A

Summary

CLEC17A (C-type lectin domain containing 17A, HGNC:34520) is a protein-coding gene on chromosome 19p13.12, encoding C-type lectin domain family 17, member A (Q6ZS10). Cell surface receptor which may be involved in carbohydrate-mediated communication between cells in the germinal center.

Enables D-mannose binding activity; fucose binding activity; and identical protein binding activity. Predicted to be involved in immune response. Located in cell surface.

Source: NCBI Gene 388512 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_001204118

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34520
Approved symbol	CLEC17A
Name	C-type lectin domain containing 17A
Location	19p13.12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ45910
Ensembl gene	ENSG00000187912
Ensembl biotype	protein_coding
OMIM	616838
Entrez	388512

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 nonsense_mediated_decay, 2 protein_coding

ENST00000339847, ENST00000417570, ENST00000547437, ENST00000551730

RefSeq mRNA: 2 — MANE Select: NM_001204118 NM_001204118, NM_207390

CCDS: CCDS46002, CCDS56087

Canonical transcript exons

ENST00000417570 — 14 exons

Exon	Start	End
ENSE00001364460	14594759	14594800
ENSE00001366023	14597099	14597161
ENSE00001367086	14595274	14595315
ENSE00001370388	14594517	14594549
ENSE00001370582	14594632	14594682
ENSE00001377865	14599717	14599812
ENSE00001384218	14596876	14597013
ENSE00001723845	14587614	14587691
ENSE00001797386	14592281	14592358
ENSE00001801141	14583357	14583434
ENSE00003541853	14600031	14600182
ENSE00003580568	14610064	14612035
ENSE00003687150	14606993	14607102
ENSE00003903772	14583084	14583203

Expression profiles

Bgee: expression breadth broad, 92 present calls, max score 84.26.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.6136 / max 189.8332, expressed in 145 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174278	1.6136	145

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lymph node	UBERON:0000029	84.26	gold quality
vermiform appendix	UBERON:0001154	80.90	gold quality
spleen	UBERON:0002106	80.13	gold quality
granulocyte	CL:0000094	79.10	gold quality
blood	UBERON:0000178	78.66	gold quality
tonsil	UBERON:0002372	68.41	gold quality
leukocyte	CL:0000738	67.57	gold quality
monocyte	CL:0000576	66.40	gold quality
bone marrow cell	CL:0002092	65.49	silver quality
bone marrow	UBERON:0002371	64.21	gold quality
small intestine Peyer’s patch	UBERON:0003454	60.87	gold quality
small intestine	UBERON:0002108	59.99	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	58.45	gold quality
gall bladder	UBERON:0002110	57.90	gold quality
mucosa of transverse colon	UBERON:0004991	57.20	gold quality
rectum	UBERON:0001052	56.51	gold quality
duodenum	UBERON:0002114	54.54	gold quality
substantia nigra	UBERON:0002038	54.00	gold quality
colonic epithelium	UBERON:0000397	53.84	silver quality
stromal cell of endometrium	CL:0002255	52.41	silver quality
hypothalamus	UBERON:0001898	48.15	gold quality
testis	UBERON:0000473	47.93	gold quality
prefrontal cortex	UBERON:0000451	47.36	gold quality
right testis	UBERON:0004534	47.36	gold quality
intestine	UBERON:0000160	46.76	gold quality
left testis	UBERON:0004533	46.56	gold quality
superior frontal gyrus	UBERON:0002661	46.44	silver quality
liver	UBERON:0002107	46.42	gold quality
Ammon’s horn	UBERON:0001954	46.23	gold quality
urinary bladder	UBERON:0001255	45.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting CLEC17A, 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-5692A	100.00	74.40	6850
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-548AQ-5P	99.94	71.34	3426

Literature-anchored findings (GeneRIF, showing 2)

• this novel receptor has the potential to function in carbohydrate-mediated communication between cells in the germinal center (PMID:19419970)
• High CLEC17A expression is associated with breast cancer. (PMID:26908442)

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	tfc	FBGN0035199
drosophila_melanogaster	CG14866	FBGN0038315
drosophila_melanogaster	lectin-46Cb	FBGN0040092
drosophila_melanogaster	lectin-46Ca	FBGN0040093
drosophila_melanogaster	lectin-33A	FBGN0040096
drosophila_melanogaster	CG34033	FBGN0054033
caenorhabditis_elegans	clec-87	WBGENE00007709
caenorhabditis_elegans	clec-91	WBGENE00014117
caenorhabditis_elegans		WBGENE00016088
caenorhabditis_elegans		WBGENE00019606

Paralogs (14): CD209 (ENSG00000090659), FCER2 (ENSG00000104921), CLEC4M (ENSG00000104938), CLEC4A (ENSG00000111729), CD207 (ENSG00000116031), CLEC10A (ENSG00000132514), ASGR1 (ENSG00000141505), CLEC4F (ENSG00000152672), ASGR2 (ENSG00000161944), CLEC4E (ENSG00000166523), CLEC4D (ENSG00000166527), CLEC4G (ENSG00000182566), CLEC4C (ENSG00000198178), CLEC6A (ENSG00000205846)

Protein

Protein identifiers

C-type lectin domain family 17, member A — Q6ZS10 (reviewed: Q6ZS10)

Alternative names: Prolectin

All UniProt accessions (2): F8W1T8, Q6ZS10

UniProt curated annotations — full annotation on UniProt →

Function. Cell surface receptor which may be involved in carbohydrate-mediated communication between cells in the germinal center. Binds glycans with terminal alpha-linked mannose or fucose residues.

Subunit / interactions. Oligomer; disulfide-linked.

Subcellular location. Membrane.

Tissue specificity. Expressed on dividing B-cells of germinal centers in various tissues, including lymph nodes, tonsils, stomach, intestine, appendix and spleen.

Post-translational modifications. Phosphorylated on tyrosine residues.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6ZS10-1	1	yes
Q6ZS10-2	2
Q6ZS10-3	3

RefSeq proteins (2): NP_001191047, NP_997273 (=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
IPR018378	C-type_lectin_CS	Conserved_site
IPR033989	CD209-like_CTLD	Domain
IPR050111	C-type_lectin/snaclec_domain	Family

Pfam: PF00059

UniProt features (25 total): binding site 5, splice variant 4, compositionally biased region 4, glycosylation site 3, disulfide bond 3, topological domain 2, chain 1, transmembrane region 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZS10-F1	71.08	0.43

Functional residue map

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

Ligand- & substrate-binding residues (5): 341; 343; 348; 360; 361

Disulfide bonds (3): 254–265, 282–372, 350–364

Glycosylation sites (3): 215, 237, 285

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): GOCC_CELL_SURFACE, GOCC_SIDE_OF_MEMBRANE, chr19p13, GOMF_D_MANNOSE_BINDING, GOCC_EXTERNAL_SIDE_OF_PLASMA_MEMBRANE, GOMF_PATTERN_RECOGNITION_RECEPTOR_ACTIVITY, GOMF_FUCOSE_BINDING, SKIL_TARGET_GENES, MIR6124, MIR873_5P, MIR323B_3P, MIR4652_5P, RYAN_MANTLE_CELL_LYMPHOMA_NOTCH_DIRECT_UP, DESCARTES_FETAL_CEREBRUM_MICROGLIA, HOWARD_MONOCYTE_INACT_MONOV_INFLUENZA_A_INDONESIA_05_2005_H5N1_AGE_18_49YO_1DY_UP

GO Biological Process (1): immune response (GO:0006955)

GO Molecular Function (7): D-mannose binding (GO:0005537), pattern recognition receptor activity (GO:0038187), identical protein binding (GO:0042802), fucose binding (GO:0042806), metal ion binding (GO:0046872), protein binding (GO:0005515), carbohydrate binding (GO:0030246)

GO Cellular Component (3): external side of plasma membrane (GO:0009897), cell surface (GO:0009986), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
monosaccharide binding	2
binding	2
cellular anatomical structure	2
immune system process	1
response to stimulus	1
signaling receptor activity	1
protein binding	1
cation binding	1
plasma membrane	1
cell surface	1
side of membrane	1

Protein interactions and networks

STRING

418 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC17A	NIBAN3	Q86XR2	511
CLEC17A	ZSWIM8	A7E2V4	483
CLEC17A	GRB2	P29354	464
CLEC17A	MRPS14	O60783	462
CLEC17A	DDX52	Q9Y2R4	449
CLEC17A	TMCC3	Q9ULS5	445
CLEC17A	PRL	P01236	432
CLEC17A	ZBTB44	Q8NCP5	417
CLEC17A	LAX1	Q8IWV1	410
CLEC17A	SLC15A2	Q16348	402
CLEC17A	ECM1	Q16610	393
CLEC17A	GRAPL	Q8TC17	386
CLEC17A	BMS1	Q14692	381
CLEC17A	MTRNR2L3	P0CJ70	370
CLEC17A	TAF9B	Q9HBM6	365

IntAct

73 interactions, top by confidence:

A	B	Type	Score
IGFBP5	CLEC17A	psi-mi:“MI:0915”(physical association)	0.600
CLEC17A	RPRM	psi-mi:“MI:0915”(physical association)	0.600
CLEC17A	FAM3C	psi-mi:“MI:0915”(physical association)	0.560
NCK2	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CTXN3	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CLDN8	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CLEC17A	TMEM140	psi-mi:“MI:0915”(physical association)	0.560
TMEM201	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
UPK2	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
SEC23A	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
TM4SF4	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CLEC17A	NINJ2	psi-mi:“MI:0915”(physical association)	0.560
CLEC17A	SMIM3	psi-mi:“MI:0915”(physical association)	0.560
OLFM4	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CLEC17A	PELI1	psi-mi:“MI:0915”(physical association)	0.560
CLEC17A	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
TMEM218	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CLEC17A	PELI2	psi-mi:“MI:0915”(physical association)	0.560
ATP6V0C	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
ASGR2	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
CLEC17A	GPR152	psi-mi:“MI:0915”(physical association)	0.560
CXCL9	CLEC17A	psi-mi:“MI:0915”(physical association)	0.560
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
FAM3C	CLEC17A	psi-mi:“MI:0915”(physical association)	0.000
NCK2	CLEC17A	psi-mi:“MI:0915”(physical association)	0.000
IGFBP5	CLEC17A	psi-mi:“MI:0915”(physical association)	0.000
CTXN3	CLEC17A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid), CLEC17A (Two-hybrid)

ESM2 similar proteins: A6H6E2, A6QQC6, O43278, O55034, O88324, O89103, P02707, P06734, P0C6B7, P10716, P20693, P21757, P30203, P30204, P41274, P47970, P60883, P70194, P86176, Q01151, Q05585, Q5DID0, Q5DID3, Q5RFW0, Q61003, Q64335, Q6ZS10, Q6ZU45, Q86T13, Q8CFD9, Q8CJ91, Q8HY02, Q8HY04, Q8MIS5, Q8N1N0, Q8VCP9, Q91ZV2, Q91ZW7, Q91ZW8, Q91ZX1

Diamond homologs: A0ZT93, B0VXV2, B4XT08, B5U6Y6, B5U6Y7, C0HKZ7, O60449, P05140, P06027, P06734, P0DJL5, P10716, P13611, P14371, P20693, P34472, P55066, P55067, P81018, P81282, P81996, Q01758, Q02988, Q26627, Q28062, Q28670, Q28858, Q4PRD0, Q4TU93, Q4V885, Q61830, Q62059, Q64449, Q66S03, Q6X5S2, Q6X5S3, Q6X5S5, Q6X5S6, Q6X5S7, Q6X5S8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1938 predictions. Top by Δscore:

Variant	Effect	Δscore
19:14592275:T:TA	acceptor_gain	1.0000
19:14592276:GGAAG:G	acceptor_loss	1.0000
19:14592277:GAAGG:G	acceptor_loss	1.0000
19:14592279:A:AC	acceptor_loss	1.0000
19:14592279:A:AG	acceptor_gain	1.0000
19:14592279:AG:A	acceptor_gain	1.0000
19:14592280:G:GG	acceptor_gain	1.0000
19:14592280:G:GT	acceptor_loss	1.0000
19:14592280:GG:G	acceptor_gain	1.0000
19:14597012:GT:G	donor_gain	1.0000
19:14597097:A:AG	acceptor_gain	1.0000
19:14597098:G:GG	acceptor_gain	1.0000
19:14597160:TA:T	donor_gain	1.0000
19:14600179:GCAC:G	donor_gain	1.0000
19:14600183:G:GG	donor_gain	1.0000
19:14583351:T:TA	acceptor_gain	0.9900
19:14583356:G:A	acceptor_gain	0.9900
19:14583430:GCCAG:G	donor_gain	0.9900
19:14583435:GTAA:G	donor_loss	0.9900
19:14583436:T:A	donor_loss	0.9900
19:14587608:T:TA	acceptor_gain	0.9900
19:14587609:G:A	acceptor_gain	0.9900
19:14587609:GGAA:G	acceptor_loss	0.9900
19:14587610:GAA:G	acceptor_loss	0.9900
19:14587612:A:AG	acceptor_gain	0.9900
19:14587612:AG:A	acceptor_gain	0.9900
19:14587613:G:GA	acceptor_loss	0.9900
19:14587613:G:GG	acceptor_gain	0.9900
19:14587613:GG:G	acceptor_gain	0.9900
19:14592276:G:A	acceptor_gain	0.9900

AlphaMissense

2481 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:14610070:G:C	W337C	0.999
19:14610070:G:T	W337C	0.999
19:14600132:T:A	C282S	0.998
19:14600133:G:A	C282Y	0.998
19:14600133:G:C	C282S	0.998
19:14600134:C:G	C282W	0.998
19:14607070:G:C	W324C	0.998
19:14607070:G:T	W324C	0.998
19:14607076:G:C	W326C	0.998
19:14607076:G:T	W326C	0.998
19:14610134:T:A	W359R	0.998
19:14610134:T:C	W359R	0.998
19:14610136:G:C	W359C	0.998
19:14610136:G:T	W359C	0.998
19:14600113:G:C	W275C	0.997
19:14600113:G:T	W275C	0.997
19:14600132:T:C	C282R	0.997
19:14607074:T:A	W326R	0.997
19:14607074:T:C	W326R	0.997
19:14610107:T:A	C350S	0.997
19:14610108:G:C	C350S	0.997
19:14610174:G:A	C372Y	0.997
19:14600133:G:T	C282F	0.996
19:14607068:T:A	W324R	0.996
19:14607068:T:C	W324R	0.996
19:14610107:T:C	C350R	0.996
19:14610175:T:G	C372W	0.996
19:14600062:G:C	W258C	0.995
19:14600062:G:T	W258C	0.995
19:14600154:T:C	L289S	0.995

dbSNP variants (sampled 300 via entrez): RS1000087526 (19:14609399 A>G), RS1000109830 (19:14579227 G>A), RS1000156985 (19:14582027 C>A), RS1000335974 (19:14589547 C>T), RS1000436052 (19:14594883 AT>A,ATT), RS1000475283 (19:14579464 C>T), RS1000532207 (19:14611283 A>G), RS1000542829 (19:14609060 A>C), RS1000651589 (19:14605161 G>A,T), RS1000760448 (19:14605507 A>G), RS1000969202 (19:14581311 A>G), RS1000988047 (19:14586245 C>T), RS1001104778 (19:14580996 G>A,T), RS1001149508 (19:14610750 G>A,C), RS1001181124 (19:14580191 G>A,T)

Disease associations

OMIM: gene MIM:616838 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST007059_3	Response to antidepressants (symptom improvement)	5.000000e-06
GCST007743_4	Iris color (L* coordinate)	5.000000e-06
GCST011346_38	Total cholesterol levels	3.000000e-14
GCST011347_58	Low density lipoprotein cholesterol levels	2.000000e-17
GCST012490_75	Femur bone mineral density x serum urate levels interaction	1.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009764	eye colour measurement
EFO:0004574	total cholesterol measurement
EFO:0004611	low density lipoprotein cholesterol 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
Benzo(a)pyrene	affects methylation	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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