CLEC1A

Summary

CLEC1A (C-type lectin domain family 1 member A, HGNC:24355) is a protein-coding gene on chromosome 12p13.2, encoding C-type lectin domain family 1 member A (Q8NC01).

This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The encoded protein may play a role in regulating dendritic cell function. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 51267 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_016511

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24355
Approved symbol	CLEC1A
Name	C-type lectin domain family 1 member A
Location	12p13.2
Locus type	gene with protein product
Status	Approved
Aliases	CLEC1, CLEC-1, MGC34328
Ensembl gene	ENSG00000150048
Ensembl biotype	protein_coding
OMIM	606782
Entrez	51267

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 nonsense_mediated_decay

ENST00000315330, ENST00000414501, ENST00000420265, ENST00000457018, ENST00000544104, ENST00000902292

RefSeq mRNA: 5 — MANE Select: NM_016511 NM_001297748, NM_001297749, NM_001297750, NM_001297751, NM_016511

CCDS: CCDS73443, CCDS76528, CCDS8612

Canonical transcript exons

ENST00000315330 — 6 exons

Exon	Start	End
ENSE00000993561	10073293	10073411
ENSE00000993562	10075504	10075655
ENSE00000993563	10081237	10081413
ENSE00001179941	10069554	10071513
ENSE00001234709	10098808	10098985
ENSE00003499598	10089124	10089222

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 88.56.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7332 / max 96.9353, expressed in 338 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
129466	0.9301	278
129465	0.4400	188
129467	0.2874	139
129468	0.0507	17
129464	0.0251	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
placenta	UBERON:0001987	88.56	gold quality
upper lobe of left lung	UBERON:0008952	86.82	gold quality
upper lobe of lung	UBERON:0008948	86.09	gold quality
right lung	UBERON:0002167	85.66	gold quality
omental fat pad	UBERON:0010414	84.64	gold quality
peritoneum	UBERON:0002358	84.52	gold quality
subcutaneous adipose tissue	UBERON:0002190	83.73	gold quality
adipose tissue of abdominal region	UBERON:0007808	83.60	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.30	gold quality
tibial nerve	UBERON:0001323	81.59	gold quality
lung	UBERON:0002048	80.92	gold quality
body of uterus	UBERON:0009853	80.78	gold quality
endocervix	UBERON:0000458	80.58	gold quality
adipose tissue	UBERON:0001013	79.92	gold quality
ectocervix	UBERON:0012249	79.31	gold quality
left uterine tube	UBERON:0001303	79.18	gold quality
mucosa of stomach	UBERON:0001199	78.74	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.69	gold quality
connective tissue	UBERON:0002384	78.44	gold quality
smooth muscle tissue	UBERON:0001135	77.27	gold quality
left lobe of thyroid gland	UBERON:0001120	76.99	gold quality
gall bladder	UBERON:0002110	76.52	gold quality
apex of heart	UBERON:0002098	76.47	gold quality
lower esophagus muscularis layer	UBERON:0035833	76.35	gold quality
lower esophagus	UBERON:0013473	76.33	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.31	gold quality
thyroid gland	UBERON:0002046	76.17	gold quality
right ovary	UBERON:0002118	76.05	gold quality
right atrium auricular region	UBERON:0006631	75.91	gold quality
right lobe of thyroid gland	UBERON:0001119	75.81	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	11.17
E-ANND-3	yes	9.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

113 targeting CLEC1A, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-3663-3P	99.84	70.39	798

Literature-anchored findings (GeneRIF, showing 3)

• Expression of CLEC-1 mRNA was detected in myeloid cells as well as in endothelial cells. CLEC-1 protein displayed N-linked glycosylation and formed dimers. (PMID:22117783)
• Histidine-Rich Glycoprotein Stimulates Human Neutrophil Phagocytosis and Prolongs Survival through CLEC1A. (PMID:33452125)
• CLEC-1 Acts as a Negative Regulator of Dectin-1 Induced Host Inflammatory Response Signature in Aspergillus fumigatus Keratitis. (PMID:34043748)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-193e13.5	ENSDARG00000052656
danio_rerio		ENSDARG00000074732
danio_rerio	si:dkey-26c10.5	ENSDARG00000088023
danio_rerio	si:ch211-170d8.8	ENSDARG00000090945
mus_musculus	Clec1a	ENSMUSG00000033082
rattus_norvegicus	Clec1a	ENSRNOG00000060460
drosophila_melanogaster	rgn	FBGN0261258
caenorhabditis_elegans		WBGENE00009156
caenorhabditis_elegans		WBGENE00013008

Paralogs (23): CLEC2D (ENSG00000069493), CD69 (ENSG00000110848), CLEC2B (ENSG00000110852), KLRB1 (ENSG00000111796), KLRD1 (ENSG00000134539), KLRC1 (ENSG00000134545), KLRG1 (ENSG00000139187), KLRF1 (ENSG00000150045), CLEC1B (ENSG00000165682), CLEC7A (ENSG00000172243), CLEC12A (ENSG00000172322), OLR1 (ENSG00000173391), KLRC4 (ENSG00000183542), CLEC2A (ENSG00000188393), KLRG2 (ENSG00000188883), CLEC9A (ENSG00000197992), KLRC2 (ENSG00000205809), KLRC3 (ENSG00000205810), KLRK1 (ENSG00000213809), CLEC2L (ENSG00000236279), CLEC12B (ENSG00000256660), KLRF2 (ENSG00000256797), CLEC5A (ENSG00000258227)

Protein

Protein identifiers

C-type lectin domain family 1 member A — Q8NC01 (reviewed: Q8NC01)

Alternative names: C-type lectin-like receptor 1

All UniProt accessions (5): Q8NC01, E7ESV9, E9PFB4, F5H038, F8WCT4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Expressed preferentially in dendritic cells.

RefSeq proteins (5): NP_001284677, NP_001284678, NP_001284679, NP_001284680, NP_057595* (*=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
IPR033992	NKR-like_CTLD	Domain
IPR052309	C-type_Lectin_Domain_Fam1	Family

Pfam: PF00059

UniProt features (14 total): topological domain 2, disulfide bond 2, compositionally biased region 2, glycosylation site 2, chain 1, sequence variant 1, sequence conflict 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-Q8NC01-F1	84.51	0.68

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 (2): 165–257, 236–249

Glycosylation sites (2): 95, 169

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): TAATAAT_MIR126, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, CUI_TCF21_TARGETS_2_DN, BOQUEST_STEM_CELL_DN, TGGAAA_NFAT_Q4_01, GOMF_TRANSMEMBRANE_SIGNALING_RECEPTOR_ACTIVITY, HATADA_METHYLATED_IN_LUNG_CANCER_UP, P53_DN.V2_UP, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_DN, GSE13522_WT_VS_IFNG_KO_SKIN_UP, MIR4795_3P, MIR23A_3P_MIR23B_3P, MIR23C, MIR126_5P, MIR3919

GO Biological Process (2): signal transduction (GO:0007165), cell surface receptor signaling pathway (GO:0007166)

GO Molecular Function (3): transmembrane signaling receptor activity (GO:0004888), carbohydrate binding (GO:0030246), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
signal transduction	1
signaling receptor activity	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

650 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC1A	CLEC4E	Q9ULY5	729
CLEC1A	REG1B	P48304	711
CLEC1A	REG1A	P05451	650
CLEC1A	KLRC4	O43908	634
CLEC1A	CLEC4G	Q6UXB4	595
CLEC1A	CLEC4D	Q8WXI8	578
CLEC1A	ASGR1	P07306	550
CLEC1A	PDPN	Q86YL7	524
CLEC1A	CLEC6A	Q6EIG7	449
CLEC1A	NLRP11	P59045	447
CLEC1A	CLECL1	Q8IZS7	420
CLEC1A	CLEC2D	Q9UHP7	403
CLEC1A	PGLYRP1	O75594	382
CLEC1A	CD209	Q9NNX6	350
CLEC1A	SCGB1D2	O95969	341

IntAct

42 interactions, top by confidence:

A	B	Type	Score
CLEC1A	LRRC4C	psi-mi:“MI:0915”(physical association)	0.560
STX1A	CLEC1A	psi-mi:“MI:0915”(physical association)	0.560
TRAM1L1	CLEC1A	psi-mi:“MI:0915”(physical association)	0.560
CLEC12A	CLEC1A	psi-mi:“MI:0915”(physical association)	0.560
CLEC1A	GPR152	psi-mi:“MI:0915”(physical association)	0.560
CLEC1A	CERS4	psi-mi:“MI:0915”(physical association)	0.560
LRRC25	CLEC1A	psi-mi:“MI:0915”(physical association)	0.560
FFAR2	CLEC1A	psi-mi:“MI:0915”(physical association)	0.560
RNF19B	CLEC1A	psi-mi:“MI:0915”(physical association)	0.560
CLEC1A	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
CLEC1A	MRPS18B	psi-mi:“MI:0915”(physical association)	0.560
CLEC1A	GPX8	psi-mi:“MI:0915”(physical association)	0.560
GJA8	CLEC1A	psi-mi:“MI:0915”(physical association)	0.560
CLEC1A	CCPG1	psi-mi:“MI:0915”(physical association)	0.400
CREB3	CLEC1A	psi-mi:“MI:0915”(physical association)	0.370
TRAM1L1	CLEC1A	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	STX1A	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	CLEC12A	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	CERS4	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	LRRC25	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	FFAR2	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	RNF19B	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	GJA8	psi-mi:“MI:0915”(physical association)	0.000
CLEC1A	GPR152	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (18): CCPG1 (Affinity Capture-MS), CCPG1 (Affinity Capture-MS), CLEC1A (Two-hybrid), CLEC1A (Synthetic Lethality), CLEC1A (Two-hybrid), CLEC1A (Two-hybrid), CLEC1A (Two-hybrid), CLEC1A (Two-hybrid), CLEC1A (Two-hybrid), CLEC1A (Two-hybrid), GPX8 (Two-hybrid), CLEC12A (Two-hybrid), FNDC9 (Two-hybrid), TRAM1L1 (Two-hybrid), LRRC25 (Two-hybrid)

ESM2 similar proteins: A4KWA1, D3W0D1, D4AD02, O54709, O70215, O88713, P20937, P26715, P27471, P27811, P27812, P27814, Q07108, Q0ZUP0, Q0ZUP1, Q12918, Q149M0, Q2HXU8, Q2NL33, Q5NKN2, Q5NKN4, Q5QGZ9, Q60652, Q60654, Q63378, Q64335, Q67EQ0, Q6QLQ4, Q6UXN8, Q80XD9, Q80ZC8, Q8BRU4, Q8BWY2, Q8C1T8, Q8CJC7, Q8MI05, Q8NC01, Q8VD98, Q8VI21, Q95MI5

Diamond homologs: A3FM55, B4XSY4, B4XSZ2, B4XSZ3, B4XSZ4, B4XSZ5, B4XSZ6, B4XSZ7, B4XSZ9, D4AD02, O35778, O54707, O54709, O70156, O70215, P07897, P08290, P10716, P13608, P16112, P24721, P26715, P26717, P26718, P27812, P27814, P34927, P49300, P60883, P61252, P78380, P79391, P81112, P81397, Q09GK0, Q0VCS6, Q12918, Q13241, Q149M0, Q28670

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	9
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1256 predictions. Top by Δscore:

Variant	Effect	Δscore
12:10073291:A:AC	donor_gain	1.0000
12:10073292:C:CC	donor_gain	1.0000
12:10073292:CAGTT:C	donor_gain	1.0000
12:10071515:T:C	acceptor_gain	0.9900
12:10089122:A:AC	donor_gain	0.9900
12:10089123:C:CC	donor_gain	0.9900
12:10089123:CA:C	donor_gain	0.9900
12:10098803:GGTAC:G	donor_loss	0.9900
12:10098804:GTA:G	donor_loss	0.9900
12:10098805:TACCT:T	donor_loss	0.9900
12:10098806:A:AT	donor_loss	0.9900
12:10098807:CCTGT:C	donor_loss	0.9900
12:10071514:C:A	acceptor_loss	0.9800
12:10071515:T:A	acceptor_loss	0.9800
12:10073292:CA:C	donor_gain	0.9800
12:10075657:T:C	acceptor_gain	0.9700
12:10075657:T:TC	acceptor_gain	0.9700
12:10089223:C:CC	acceptor_gain	0.9700
12:10098754:T:TA	donor_gain	0.9700
12:10071512:ACCTT:A	acceptor_gain	0.9600
12:10073292:CAG:C	donor_gain	0.9600
12:10075497:ATCTT:A	donor_loss	0.9600
12:10075498:TCTTA:T	donor_loss	0.9600
12:10075499:CTTA:C	donor_loss	0.9600
12:10075500:TTA:T	donor_loss	0.9600
12:10075501:T:TG	donor_loss	0.9600
12:10075502:AC:A	donor_loss	0.9600
12:10081230:CACTT:C	donor_loss	0.9600
12:10081231:ACTT:A	donor_loss	0.9600
12:10081232:CTTA:C	donor_loss	0.9600

AlphaMissense

1854 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:10073364:C:A	W197C	0.996
12:10073364:C:G	W197C	0.996
12:10073322:C:A	W211C	0.995
12:10073322:C:G	W211C	0.995
12:10075573:C:A	W158C	0.995
12:10075573:C:G	W158C	0.995
12:10075624:C:A	W141C	0.994
12:10075624:C:G	W141C	0.994
12:10073328:C:A	W209C	0.991
12:10073328:C:G	W209C	0.991
12:10075553:C:G	C165S	0.990
12:10075554:A:T	C165S	0.990
12:10075604:C:G	C148S	0.989
12:10075605:A:T	C148S	0.989
12:10071468:A:C	C236W	0.988
12:10075618:C:A	W143C	0.988
12:10075618:C:G	W143C	0.988
12:10071469:C:G	C236S	0.987
12:10071470:A:T	C236S	0.987
12:10071406:C:G	C257S	0.984
12:10071407:A:T	C257S	0.984
12:10073366:A:G	W197R	0.984
12:10073366:A:T	W197R	0.984
12:10075552:G:C	C165W	0.983
12:10071469:C:T	C236Y	0.982
12:10075553:C:T	C165Y	0.982
12:10075565:C:T	C161Y	0.982
12:10075603:G:C	C148W	0.982
12:10071430:C:G	C249S	0.981
12:10071431:A:T	C249S	0.981

dbSNP variants (sampled 300 via entrez): RS1000153633 (12:10083878 A>G), RS1000204271 (12:10086538 G>A,C), RS1000219364 (12:10087966 C>G,T), RS1000306099 (12:10077481 G>A), RS1000358787 (12:10077289 T>C), RS1000401645 (12:10081126 C>T), RS1000519420 (12:10090744 G>A), RS1000573501 (12:10090515 C>T), RS1000773057 (12:10100820 A>C,G,T), RS1000780094 (12:10097515 A>T), RS1000816326 (12:10080941 G>T), RS1000870466 (12:10083766 T>C), RS1001079983 (12:10094595 A>G), RS1001128958 (12:10097843 T>C), RS1001260220 (12:10086933 C>T)

Disease associations

OMIM: gene MIM:606782 | disease phenotypes: MIM:614079

GenCC curated gene-disease

Mondo (1): aspergillosis, susceptibility to (MONDO:0013562)

Orphanet (1): Aspergillosis (Orphanet:1163)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009391_1646	Metabolite levels	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007787	plasma betaine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, decreases methylation, increases expression, affects methylation	2
cobaltous chloride	decreases expression	1
perfluoro-n-nonanoic acid	affects expression	1
Pioglitazone	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	increases methylation	1
Tretinoin	increases expression	1
Valproic Acid	increases expression	1
Zinc	decreases expression	1
beta-Naphthoflavone	decreases expression	1

Clinical trials (associated diseases)

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