CLEC4F

Summary

CLEC4F (C-type lectin domain family 4 member F, HGNC:25357) is a protein-coding gene on chromosome 2p13.3, encoding C-type lectin domain family 4 member F (Q8N1N0). Receptor with an affinity for galactose and fucose.

Predicted to enable galactose binding activity; glycolipid binding activity; and pattern recognition receptor activity. Predicted to be involved in immune response. Predicted to act upstream of or within NK T cell activation. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane.

Source: NCBI Gene 165530 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_173535

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25357
Approved symbol	CLEC4F
Name	C-type lectin domain family 4 member F
Location	2p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39110, KCLR
Ensembl gene	ENSG00000152672
Ensembl biotype	protein_coding
OMIM	620105
Entrez	165530

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000272367, ENST00000426626

RefSeq mRNA: 3 — MANE Select: NM_173535 NM_001258027, NM_001321308, NM_173535

CCDS: CCDS1910, CCDS82464

Canonical transcript exons

ENST00000272367 — 7 exons

Exon	Start	End
ENSE00000963091	70812447	70812598
ENSE00000963092	70809739	70809857
ENSE00001006555	70815994	70817112
ENSE00001241456	70808643	70809382
ENSE00001241475	70819355	70819444
ENSE00001241480	70819775	70819891
ENSE00001241496	70820463	70820599

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 79.26.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1411 / max 69.8216, expressed in 31 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29044	0.1357	31
29043	0.0055	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	79.26	gold quality
leukocyte	CL:0000738	67.31	gold quality
monocyte	CL:0000576	67.09	gold quality
smooth muscle tissue	UBERON:0001135	65.68	gold quality
spleen	UBERON:0002106	65.31	gold quality
body of uterus	UBERON:0009853	63.80	gold quality
jejunal mucosa	UBERON:0000399	61.15	silver quality
apex of heart	UBERON:0002098	61.03	gold quality
gall bladder	UBERON:0002110	60.90	gold quality
omental fat pad	UBERON:0010414	60.55	gold quality
peritoneum	UBERON:0002358	60.49	gold quality
duodenum	UBERON:0002114	60.12	gold quality
skin of abdomen	UBERON:0001416	59.84	gold quality
adipose tissue of abdominal region	UBERON:0007808	59.46	gold quality
skin of leg	UBERON:0001511	59.00	gold quality
right coronary artery	UBERON:0001625	58.39	gold quality
lower esophagus	UBERON:0013473	58.27	gold quality
lower esophagus muscularis layer	UBERON:0035833	58.24	gold quality
rectum	UBERON:0001052	58.07	gold quality
skin of hip	UBERON:0001554	57.99	gold quality
endocervix	UBERON:0000458	57.58	gold quality
small intestine	UBERON:0002108	57.36	gold quality
zone of skin	UBERON:0000014	57.16	gold quality
myometrium	UBERON:0001296	57.12	gold quality
pigmented layer of retina	UBERON:0001782	57.12	silver quality
lymph node	UBERON:0000029	56.87	gold quality
small intestine Peyer’s patch	UBERON:0003454	56.78	gold quality
vagina	UBERON:0000996	56.58	gold quality
esophagus	UBERON:0001043	55.85	gold quality
vermiform appendix	UBERON:0001154	55.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting CLEC4F, 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-623	99.76	68.16	1170
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-4520-2-3P	99.14	69.28	1009
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-181A-2-3P	98.91	67.60	1168
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-5008-3P	98.73	67.50	1433
HSA-MIR-6755-3P	98.61	66.90	834
HSA-MIR-4780	98.57	64.75	611
HSA-MIR-5187-5P	98.54	67.94	952
HSA-MIR-93-3P	98.15	66.65	1309
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-4494	97.86	64.93	850
HSA-MIR-663B	97.40	62.91	664
HSA-MIR-3192-5P	96.98	65.76	1926
HSA-MIR-6729-3P	96.91	66.79	703
HSA-MIR-4436B-5P	96.71	68.37	1346
HSA-MIR-6726-5P	95.97	63.72	841
HSA-MIR-920	95.97	63.95	811
HSA-MIR-5591-5P	95.85	64.76	1002
HSA-MIR-4300	95.85	64.56	1003
HSA-MIR-3677-5P	93.16	64.62	393

Cross-species orthologs

20 orthologs

Organism	Symbol	Gene ID
danio_rerio	illr4	ENSDARG00000008075
danio_rerio	illr3	ENSDARG00000018327
danio_rerio	cldc1	ENSDARG00000056379
danio_rerio	zgc:174904	ENSDARG00000059049
danio_rerio	illr1	ENSDARG00000059254
danio_rerio	si:ch211-232p21.6	ENSDARG00000089377
danio_rerio	si:ch211-133n4.12	ENSDARG00000092749
danio_rerio	si:ch211-133n4.11	ENSDARG00000094796
danio_rerio	illr2	ENSDARG00000094882
danio_rerio	si:ch211-133n4.7	ENSDARG00000095424
mus_musculus	Clec4f	ENSMUSG00000014542
rattus_norvegicus	Clec4f	ENSRNOG00000013137
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), ASGR2 (ENSG00000161944), CLEC4E (ENSG00000166523), CLEC4D (ENSG00000166527), CLEC4G (ENSG00000182566), CLEC17A (ENSG00000187912), CLEC4C (ENSG00000198178), CLEC6A (ENSG00000205846)

Protein

Protein identifiers

C-type lectin domain family 4 member F — Q8N1N0 (reviewed: Q8N1N0)

Alternative names: C-type lectin superfamily member 13

All UniProt accessions (1): Q8N1N0

UniProt curated annotations — full annotation on UniProt →

Function. Receptor with an affinity for galactose and fucose. Could be involved in endocytosis.

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N1N0-1	1	yes
Q8N1N0-2	2

RefSeq proteins (3): NP_001244956, NP_001308237, NP_775806* (*=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
IPR033989	CD209-like_CTLD	Domain
IPR050111	C-type_lectin/snaclec_domain	Family

Pfam: PF00059

UniProt features (18 total): glycosylation site 8, sequence variant 3, topological domain 2, chain 1, splice variant 1, sequence conflict 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N1N0-F1	73.95	0.20

Functional residue map

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

Glycosylation sites (8): 312, 385, 399, 79, 113, 207, 230, 244

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOCC_CELL_SURFACE, GOBP_VESICLE_MEDIATED_TRANSPORT, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GOBP_IMPORT_INTO_CELL, GOBP_ENDOCYTOSIS, GOCC_SIDE_OF_MEMBRANE, DODD_NASOPHARYNGEAL_CARCINOMA_DN, chr2p13, GOCC_EXTERNAL_SIDE_OF_PLASMA_MEMBRANE, GUILLAUMOND_KLF10_TARGETS_DN, GOMF_PATTERN_RECOGNITION_RECEPTOR_ACTIVITY, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP, GSE10239_MEMORY_VS_KLRG1HIGH_EFF_CD8_TCELL_UP, MIR6071

GO Biological Process (2): endocytosis (GO:0006897), immune response (GO:0006955)

GO Molecular Function (2): carbohydrate binding (GO:0030246), pattern recognition receptor activity (GO:0038187)

GO Cellular Component (2): external side of plasma membrane (GO:0009897), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
immune system process	1
response to stimulus	1
binding	1
signaling receptor activity	1
plasma membrane	1
cell surface	1
side of membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

650 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC4F	VSIG4	Q9Y279	669
CLEC4F	TIMD4	Q96H15	642
CLEC4F	CD5L	O43866	617
CLEC4F	STAB2	Q8WWQ8	511
CLEC4F	LYVE1	Q9Y5Y7	474
CLEC4F	CD207	Q9UJ71	460
CLEC4F	CD68	P34810	440
CLEC4F	CCR2	P41597	434
CLEC4F	CLEC4G	Q6UXB4	408
CLEC4F	XCR1	P46094	401
CLEC4F	CSF1R	P07333	395
CLEC4F	HP	P00737	392
CLEC4F	CLEC1B	Q9P126	391
CLEC4F	ITGAM	P11215	389
CLEC4F	FGD4	Q96M96	383

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CLEC4F	ITGAV	psi-mi:“MI:0914”(association)	0.350
	CLEC4F	psi-mi:“MI:0915”(physical association)	0.000
ATXN1	CLEC4F	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (9): CLEC4F (Proximity Label-MS), CD207 (Affinity Capture-MS), CSGALNACT2 (Affinity Capture-MS), COLEC12 (Affinity Capture-MS), NPTX2 (Affinity Capture-MS), FBXO28 (Affinity Capture-MS), ITGAV (Affinity Capture-MS), PBXIP1 (Affinity Capture-MS), CLEC4F (Two-hybrid)

ESM2 similar proteins: A4GSN8, D3ZZL9, F4HXQ7, F4HZB5, F4I8B9, F4I9A2, F4ICX9, F4JIF4, F4JJP1, F4JZY1, I0J0E7, O64584, O97961, P0C6E7, P0CB23, P17536, P30622, P61430, P93203, Q00547, Q0DY81, Q13439, Q14789, Q15643, Q25662, Q61595, Q84VY2, Q86UP2, Q8CHG3, Q8IWJ2, Q8L7E5, Q8N1N0, Q8S2T0, Q90631, Q922J3, Q99996, Q9BZF9, Q9C698, Q9CA42, Q9CAP9

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	12
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1005 predictions. Top by Δscore:

Variant	Effect	Δscore
2:70820457:TCTCA:T	donor_loss	0.9900
2:70820458:CTCAC:C	donor_loss	0.9900
2:70820459:TCA:T	donor_loss	0.9900
2:70820460:CAC:C	donor_loss	0.9900
2:70820461:A:T	donor_loss	0.9900
2:70809738:CG:C	donor_gain	0.9700
2:70819353:A:AC	donor_gain	0.9700
2:70819354:C:CC	donor_gain	0.9700
2:70820492:T:C	donor_gain	0.9700
2:70812454:T:TA	donor_gain	0.9600
2:70815992:A:AC	donor_gain	0.9600
2:70815993:C:CC	donor_gain	0.9600
2:70815993:CTTTG:C	donor_gain	0.9500
2:70820531:T:TA	donor_gain	0.9500
2:70810835:C:CA	donor_gain	0.9300
2:70820484:A:AC	donor_gain	0.9300
2:70820485:C:CC	donor_gain	0.9300
2:70809074:C:CT	acceptor_gain	0.9200
2:70809074:C:T	acceptor_gain	0.9200
2:70809075:A:T	acceptor_gain	0.9100
2:70809855:TGCC:T	acceptor_loss	0.9100
2:70809858:C:A	acceptor_loss	0.9100
2:70815993:CT:C	donor_gain	0.9100
2:70819354:CT:C	donor_gain	0.9100
2:70819774:CCCA:C	donor_gain	0.9100
2:70809081:C:T	acceptor_gain	0.9000
2:70812484:C:CA	donor_gain	0.9000
2:70812611:T:TC	acceptor_gain	0.9000
2:70809860:G:C	acceptor_loss	0.8900
2:70819354:CTGTT:C	donor_gain	0.8900

AlphaMissense

3935 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:70812509:C:G	A493P	0.974
2:70809777:C:A	W540C	0.967
2:70809777:C:G	W540C	0.967
2:70809779:A:G	W540R	0.956
2:70809779:A:T	W540R	0.956
2:70812516:C:A	W490C	0.950
2:70812516:C:G	W490C	0.950
2:70809852:A:C	F515L	0.949
2:70809852:A:T	F515L	0.949
2:70809854:A:G	F515L	0.949
2:70812567:C:A	W473C	0.942
2:70812567:C:G	W473C	0.942
2:70812495:G:C	C497W	0.939
2:70812496:C:T	C497Y	0.939
2:70809783:C:A	W538C	0.937
2:70809783:C:G	W538C	0.937
2:70812569:A:G	W473R	0.934
2:70812569:A:T	W473R	0.934
2:70812482:C:G	A502P	0.929
2:70809811:A:G	L529P	0.926
2:70809785:A:G	W538R	0.922
2:70809785:A:T	W538R	0.922
2:70809819:C:A	W526C	0.920
2:70809819:C:G	W526C	0.920
2:70812496:C:G	C497S	0.918
2:70812497:A:T	C497S	0.918
2:70812537:A:C	F483L	0.907
2:70812537:A:T	F483L	0.907
2:70812539:A:G	F483L	0.907
2:70812497:A:G	C497R	0.906

dbSNP variants (sampled 300 via entrez): RS1000251645 (2:70813083 G>A,C), RS1000832503 (2:70823597 C>T), RS1001022832 (2:70818042 C>A), RS1001317550 (2:70826465 C>A,T), RS1001687744 (2:70815573 A>G), RS1001741493 (2:70815778 G>A), RS1001761611 (2:70808766 C>T), RS1001910655 (2:70822856 C>T), RS1001931433 (2:70816569 T>C), RS1002146231 (2:70811781 A>C), RS1002214110 (2:70809017 A>G), RS1002238437 (2:70822623 G>A), RS1002548413 (2:70820078 A>C), RS1002945888 (2:70819718 G>A,C,T), RS1003663913 (2:70825128 A>G)

Disease associations

OMIM: gene MIM:620105 | 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
GCST002380_1	Erythema nodosum in inflammatory bowel disease	3.000000e-06
GCST002481_1	Acne (severe)	5.000000e-06
GCST003123_5	Severe influenza A (H1N1) infection	2.000000e-09
GCST003263_103	Post bronchodilator FEV1 in COPD	4.000000e-06
GCST003265_315	Post bronchodilator FEV1/FVC ratio in COPD	4.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:1001488	influenza A (H1N1)
EFO:0004314	forced expiratory volume
EFO:0004713	FEV/FVC ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
benzo(e)pyrene	increases methylation	1
(+)-JQ1 compound	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Methapyrilene	increases methylation	1
Nickel	decreases expression	1
Theophylline	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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