CLEC2L

Summary

CLEC2L (C-type lectin domain family 2 member L, HGNC:21969) is a protein-coding gene on chromosome 7q34, encoding C-type lectin domain family 2 member L (P0C7M8).

Predicted to enable carbohydrate binding activity. Predicted to be located in membrane.

Source: NCBI Gene 154790 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 46 total
• MANE Select transcript: NM_001080511

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21969
Approved symbol	CLEC2L
Name	C-type lectin domain family 2 member L
Location	7q34
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32986
Ensembl gene	ENSG00000236279
Ensembl biotype	protein_coding
Entrez	154790

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000422142, ENST00000520413, ENST00000521281

RefSeq mRNA: 2 — MANE Select: NM_001080511 NM_001080511, NM_001353368

CCDS: CCDS47724

Canonical transcript exons

ENST00000422142 — 5 exons

Exon	Start	End
ENSE00001730113	139523685	139524117
ENSE00001775787	139536274	139536348
ENSE00001782879	139540321	139540487
ENSE00003589421	139542021	139542121
ENSE00003611514	139544231	139544985

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 92.54.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8234 / max 60.5914, expressed in 164 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
81463	0.8234	164

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	92.54	gold quality
pons	UBERON:0000988	91.19	gold quality
right frontal lobe	UBERON:0002810	90.63	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.63	gold quality
anterior cingulate cortex	UBERON:0009835	89.85	gold quality
frontal cortex	UBERON:0001870	89.81	gold quality
neocortex	UBERON:0001950	88.57	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.57	gold quality
cerebral cortex	UBERON:0000956	85.78	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.13	gold quality
superior frontal gyrus	UBERON:0002661	84.58	gold quality
lateral nuclear group of thalamus	UBERON:0002736	84.13	gold quality
dorsal root ganglion	UBERON:0000044	83.68	gold quality
parietal lobe	UBERON:0001872	83.28	gold quality
primary visual cortex	UBERON:0002436	83.24	gold quality
postcentral gyrus	UBERON:0002581	83.17	gold quality
cerebellar vermis	UBERON:0004720	82.91	silver quality
hypothalamus	UBERON:0001898	82.66	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.17	gold quality
occipital lobe	UBERON:0002021	81.88	gold quality
nucleus accumbens	UBERON:0001882	81.41	gold quality
cerebellar cortex	UBERON:0002129	81.25	gold quality
cerebellar hemisphere	UBERON:0002245	81.19	gold quality
amygdala	UBERON:0001876	81.12	gold quality
cerebellum	UBERON:0002037	81.00	gold quality
Ammon’s horn	UBERON:0001954	80.89	gold quality
substantia nigra	UBERON:0002038	80.39	gold quality
midbrain	UBERON:0001891	80.25	gold quality
forebrain	UBERON:0001890	79.68	gold quality
brain	UBERON:0000955	79.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting CLEC2L, 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-6867-5P	100.00	82.21	3464
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-4708-3P	99.51	67.99	870
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-3166	98.24	66.63	1223
HSA-MIR-6747-3P	97.73	64.84	1596
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-4704-5P	96.13	68.67	608
HSA-MIR-6753-5P	94.70	64.08	470
HSA-MIR-4508	90.37	59.62	240
HSA-MIR-1538	85.86	60.08	75
HSA-MIR-4745-3P	83.50	60.58	126

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	Clec2l	ENSMUSG00000079598
rattus_norvegicus	Clec2l	ENSRNOG00000029644
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), CLEC1A (ENSG00000150048), CLEC1B (ENSG00000165682), CLEC7A (ENSG00000172243), CLEC12A (ENSG00000172322), OLR1 (ENSG00000173391), KLRC4 (ENSG00000183542), CLEC2A (ENSG00000188393), KLRG2 (ENSG00000188883), CLEC9A (ENSG00000197992), KLRC2 (ENSG00000205809), KLRC3 (ENSG00000205810), KLRK1 (ENSG00000213809), CLEC12B (ENSG00000256660), KLRF2 (ENSG00000256797), CLEC5A (ENSG00000258227)

Protein

Protein identifiers

C-type lectin domain family 2 member L — P0C7M8 (reviewed: P0C7M8)

All UniProt accessions (2): P0C7M8, H0YB20

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (2): NP_001073980, NP_001340297 (=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

Pfam: PF00059

UniProt features (8 total): disulfide bond 2, chain 1, transmembrane region 1, domain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7M8-F1	83.08	0.57

Functional residue map

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

Post-translational modifications (1): 32

Disulfide bonds (2): 128–208, 187–200

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, BAKKER_FOXO3_TARGETS_DN, ZNF37A_TARGET_GENES, ZNF664_TARGET_GENES, MIR6867_5P, MIR29B_3P_MIR29C_3P, MIR29A_3P, GSE10273_LOW_IL7_VS_HIGH_IL7_AND_IRF4_IN_IRF4_8_NULL_PRE_BCELL_DN, GSE15750_WT_VS_TRAF6KO_DAY10_EFF_CD8_TCELL_DN, FAN_EMBRYONIC_CTX_BIG_GROUPS_CAJAL_RETZIUS, HAY_BONE_MARROW_PLATELET, DESCARTES_MAIN_FETAL_THYMIC_EPITHELIAL_CELLS, DESCARTES_FETAL_EYE_GANGLION_CELLS, DESCARTES_FETAL_LIVER_MEGAKARYOCYTES

GO Biological Process (0):

GO Molecular Function (1): carbohydrate binding (GO:0030246)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

780 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC2L	LRRC40	Q9H9A6	512
CLEC2L	SMIM12	Q96EX1	472
CLEC2L	BEND7	Q8N7W2	458
CLEC2L	FMC1	Q96HJ9	446
CLEC2L	ZNF705A	Q6ZN79	446
CLEC2L	TCAIM	Q8N3R3	438
CLEC2L	ZC3H8	Q8N5P1	419
CLEC2L	SHISA4	Q96DD7	410
CLEC2L	BTBD8	Q5XKL5	404
CLEC2L	MNMIP1	A4FU49	401
CLEC2L	TIMM21	Q9BVV7	392
CLEC2L	NAIF1	Q69YI7	387
CLEC2L	LEPROTL1	O95214	379
CLEC2L	DNAAF8	Q8IYS4	378
CLEC2L	SNAPC3	Q92966	373

IntAct

0 interactions, top by confidence:

BioGRID (2): CLEC2L (Affinity Capture-MS), CLEC2L (Affinity Capture-MS)

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: A4D1S0, O88713, P0C7M8, P0C7M9, Q0ZCA7, Q3UM83, Q92478, Q96E93, A4KWA1, A4KWA5, A4KWA6, A4KWA8, O89335, P02706, P08290, P14371, P24721, P26715, P26717, P34927, P37217, Q07108, Q07444, Q0H8B9, Q5M9I1, Q60660, Q6EIG7, Q6QLQ4, Q6UVW9, Q6UXN8, Q80XD9, Q8BWY2, Q8C1T8, Q8HY02, Q8HY10, Q8HY11, Q8HY12, Q8IUN9, Q8MIS5, Q8N1N0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1105 predictions. Top by Δscore:

Variant	Effect	Δscore
7:139540484:GCTG:G	donor_gain	1.0000
7:139524116:GG:G	donor_gain	0.9900
7:139524117:GG:G	donor_gain	0.9900
7:139540486:TGGTG:T	donor_loss	0.9900
7:139540488:G:T	donor_loss	0.9900
7:139540489:TGAG:T	donor_loss	0.9900
7:139540490:G:GT	donor_loss	0.9900
7:139542122:G:GG	donor_gain	0.9900
7:139542127:C:G	donor_gain	0.9900
7:139544222:T:TA	acceptor_gain	0.9900
7:139540488:G:GG	donor_gain	0.9800
7:139541570:A:AG	acceptor_gain	0.9800
7:139541571:G:GG	acceptor_gain	0.9800
7:139524114:GAGG:G	donor_gain	0.9700
7:139542205:G:GT	donor_gain	0.9700
7:139544223:G:A	acceptor_gain	0.9700
7:139544226:CACA:C	acceptor_loss	0.9700
7:139544228:CA:C	acceptor_loss	0.9700
7:139540319:A:AG	acceptor_gain	0.9600
7:139540320:G:GG	acceptor_gain	0.9600
7:139542117:GACAC:G	donor_gain	0.9600
7:139544229:A:AG	acceptor_gain	0.9600
7:139544230:G:GG	acceptor_gain	0.9600
7:139524119:T:TC	donor_loss	0.9500
7:139539419:T:TA	acceptor_gain	0.9500
7:139539550:G:GA	donor_gain	0.9500
7:139539616:GTG:G	donor_gain	0.9500
7:139541571:GTAT:G	acceptor_gain	0.9500
7:139542013:C:CA	acceptor_gain	0.9500
7:139542169:GCC:G	donor_gain	0.9500

AlphaMissense

1374 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:139540367:G:C	W104C	1.000
7:139540367:G:T	W104C	1.000
7:139540386:T:A	C111S	1.000
7:139540386:T:C	C111R	1.000
7:139540387:G:C	C111S	1.000
7:139540416:T:A	W121R	1.000
7:139540416:T:C	W121R	1.000
7:139540418:G:C	W121C	1.000
7:139540418:G:T	W121C	1.000
7:139540437:T:A	C128S	1.000
7:139540438:G:A	C128Y	1.000
7:139540438:G:C	C128S	1.000
7:139540439:C:G	C128W	1.000
7:139542056:G:C	W156C	1.000
7:139542056:G:T	W156C	1.000
7:139542092:G:C	W168C	1.000
7:139542092:G:T	W168C	1.000
7:139544256:T:C	C187R	1.000
7:139536322:C:A	A80D	0.999
7:139536339:A:C	S86R	0.999
7:139536341:C:A	S86R	0.999
7:139536341:C:G	S86R	0.999
7:139540353:T:A	C100S	0.999
7:139540353:T:C	C100R	0.999
7:139540354:G:A	C100Y	0.999
7:139540354:G:C	C100S	0.999
7:139540365:T:A	W104R	0.999
7:139540365:T:C	W104R	0.999
7:139540387:G:A	C111Y	0.999
7:139540387:G:T	C111F	0.999

dbSNP variants (sampled 300 via entrez): RS1000064568 (7:139523041 G>A), RS1000073088 (7:139522561 A>G), RS1000136562 (7:139526453 G>T), RS1000222076 (7:139538873 G>A,T), RS1000346718 (7:139529134 C>T), RS1000487712 (7:139526774 T>G), RS1000495341 (7:139543653 A>C), RS1000941183 (7:139537714 G>T), RS1000943622 (7:139530717 G>C), RS1001113925 (7:139524479 G>A,C), RS1001239322 (7:139523438 C>T), RS1001411986 (7:139532677 G>A), RS1001551757 (7:139543182 C>G), RS1001723456 (7:139538474 C>T), RS1001795437 (7:139525641 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
dicrotophos	increases expression	1
Lead	affects expression	1
Triclosan	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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