CLEC10A

Summary

CLEC10A (C-type lectin domain containing 10A, HGNC:16916) is a protein-coding gene on chromosome 17p13.1, encoding C-type lectin domain family 10 member A (Q8IUN9). C-type lectin receptor involved in recognition of N-acetylgalactosamine (GalNAc)-terminated glycans by myeloid antigen presenting cells (APCs).

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 signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may function as a cell surface antigen. Two transcript variants encoding distinct isoforms have been identified for this gene.

Source: NCBI Gene 10462 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_001330070

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16916
Approved symbol	CLEC10A
Name	C-type lectin domain containing 10A
Location	17p13.1
Locus type	gene with protein product
Status	Approved
Aliases	HML2, HML, CD301
Ensembl gene	ENSG00000132514
Ensembl biotype	protein_coding
OMIM	605999
Entrez	10462

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 13 protein_coding, 1 retained_intron

ENST00000254868, ENST00000416562, ENST00000571624, ENST00000571664, ENST00000576549, ENST00000576617, ENST00000874072, ENST00000874073, ENST00000874074, ENST00000874075, ENST00000874076, ENST00000943481, ENST00000943482, ENST00000943483

RefSeq mRNA: 3 — MANE Select: NM_001330070 NM_001330070, NM_006344, NM_182906

CCDS: CCDS11087, CCDS45597, CCDS82049

Canonical transcript exons

ENST00000416562 — 9 exons

Exon	Start	End
ENSE00000905363	7075360	7075466
ENSE00000905366	7076733	7076804
ENSE00000905367	7076892	7076987
ENSE00001203744	7075731	7075885
ENSE00001285536	7077997	7078113
ENSE00001292710	7074537	7075222
ENSE00001316320	7078746	7078885
ENSE00002650608	7080052	7080251
ENSE00002682022	7075985	7076071

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 98.49.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8561 / max 462.3939, expressed in 263 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164093	1.3252	228
164094	0.3954	173
164091	0.0588	14
164089	0.0363	9
164092	0.0330	6
164090	0.0074	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.49	gold quality
secondary oocyte	CL:0000655	97.67	gold quality
granulocyte	CL:0000094	93.70	gold quality
monocyte	CL:0000576	89.69	gold quality
right coronary artery	UBERON:0001625	89.46	gold quality
leukocyte	CL:0000738	89.35	gold quality
mononuclear cell	CL:0000842	89.20	gold quality
gall bladder	UBERON:0002110	88.34	gold quality
vermiform appendix	UBERON:0001154	86.58	gold quality
rectum	UBERON:0001052	85.41	gold quality
lymph node	UBERON:0000029	83.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.74	gold quality
caecum	UBERON:0001153	82.19	gold quality
smooth muscle tissue	UBERON:0001135	80.60	gold quality
omental fat pad	UBERON:0010414	80.49	gold quality
peritoneum	UBERON:0002358	80.46	gold quality
adipose tissue of abdominal region	UBERON:0007808	79.63	gold quality
small intestine Peyer’s patch	UBERON:0003454	79.51	gold quality
blood	UBERON:0000178	79.33	gold quality
mucosa of transverse colon	UBERON:0004991	79.23	gold quality
small intestine	UBERON:0002108	79.12	gold quality
skin of hip	UBERON:0001554	78.75	gold quality
jejunal mucosa	UBERON:0000399	77.96	gold quality
upper leg skin	UBERON:0004262	77.78	gold quality
apex of heart	UBERON:0002098	77.61	gold quality
transverse colon	UBERON:0001157	77.60	gold quality
subcutaneous adipose tissue	UBERON:0002190	77.59	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.55	gold quality
esophagus squamous epithelium	UBERON:0006920	77.39	gold quality
sigmoid colon	UBERON:0001159	77.18	gold quality

Single-cell (SCXA)

Detected in 16 experiment(s), a significant marker in 16.

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	1432.58
E-MTAB-8322	yes	1174.21
E-MTAB-7381	yes	1104.83
E-MTAB-8530	yes	703.63
E-HCAD-36	yes	703.34
E-CURD-112	yes	452.77
E-HCAD-4	yes	70.22
E-HCAD-1	yes	69.93
E-CURD-46	yes	42.15
E-HCAD-10	yes	35.32
E-MTAB-6701	yes	26.16
E-CURD-88	yes	22.74
E-MTAB-10042	yes	18.35
E-MTAB-8410	yes	15.95
E-MTAB-6678	yes	8.25

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR

miRNA regulators (miRDB)

26 targeting CLEC10A, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-3606-5P	99.31	69.67	1168
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-2115-5P	98.66	68.07	1191
HSA-MIR-8060	98.61	66.93	1187
HSA-MIR-3928-5P	98.50	67.48	980
HSA-MIR-6806-3P	98.50	67.31	980
HSA-MIR-3144-3P	98.15	67.34	677
HSA-MIR-1301-5P	98.09	66.62	495
HSA-MIR-6502-5P	98.09	66.73	495
HSA-MIR-4724-3P	97.57	67.31	785
HSA-MIR-517-5P	97.13	68.43	781
HSA-MIR-6734-5P	95.70	65.56	950
HSA-MIR-1237-5P	95.38	62.21	451
HSA-MIR-4488	95.38	62.00	443
HSA-MIR-4697-5P	95.38	61.72	457
HSA-MIR-4693-3P	95.23	65.92	735
HSA-MIR-4737	89.94	65.03	82

Literature-anchored findings (GeneRIF, showing 13)

• MGL engagement improved DC performance as antigen-presenting cells, promoting the upregulation of maturation markers, a decrease in phagocytosis, an enhancement of motility, and most importantly an increase in antigen-specific CD8(+) T-cell activation. (PMID:22531918)
• Described is the use of recombinant CLEC10A (CD301), a human glycoreceptor of the C-type lectin family, for the detection of ligands in sections from formalin-fixed, paraffin-embedded normal and cancerous mammary tissues. (PMID:23275449)
• MGL triggering synergized with TLR2-induced pathways, leading to elevated IL-10 mRNA levels & enhanced TNF-alpha mRNA stability. It promoted phosphorylation of the ERK & CREB, fine-tuning the DC maturation phenotype. (PMID:23744646)
• expression of GalNAc moieties mirrors the T cell activation status, and thus only highly stimulated T cells are prone to the suppressive action of MGL. (PMID:23918927)
• These results indicate a role of MGL as an immunomodulator within the tumour microenvironment interfering with Treg functions, suggesting its possible use in the design of anticancer vaccines. (PMID:26147970)
• BRAF(V600E) mutation induces MGL ligand expression, thereby providing a direct link between oncogenic transformation and aberrant expression of immunosuppressive glycans in colorectal neoplasms. (PMID:26172302)
• this paper shows that key gene of intermediate proinflammatory monocytes, such as CLEC10A, is expressed three- to fourfold more in juvenile idiopathic arthritis-enthesitis-related arthritis (PMID:27706807)
• CLEC10A represents not only a candidate to better define CD1c(+) dendritic cells-due to its high endocytic potential-CLEC10A also exhibits an interesting candidate receptor for future antigen-targeting approaches. (PMID:29755453)
• our data provide new insight into the identification and structure of novel MGL ligands that presumably act as modulatory molecules in cancer immune responses. (PMID:30582698)
• The C-type lectin receptor MGL senses N-acetylgalactosamine on the unique Staphylococcus aureus ST395 wall teichoic acid. (PMID:31219660)
• The MGL can be used to discriminate tumor from the corresponding healthy tissues. (PMID:31911241)
• N-Glycoproteins Have a Major Role in MGL Binding to Colorectal Cancer Cell Lines: Associations with Overall Proteome Diversity. (PMID:32752259)
• High expression of CLEC10A in head and neck squamous cell carcinoma indicates favorable prognosis and high-level immune infiltration status. (PMID:35093731)

Cross-species orthologs

13 orthologs

Organism	Symbol	Gene ID
mus_musculus	Clec10a	ENSMUSG00000000318
mus_musculus	Mgl2	ENSMUSG00000040950
rattus_norvegicus	Clec10a	ENSRNOG00000018715
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), ASGR1 (ENSG00000141505), CLEC4F (ENSG00000152672), ASGR2 (ENSG00000161944), CLEC4E (ENSG00000166523), CLEC4D (ENSG00000166527), CLEC4G (ENSG00000182566), CLEC17A (ENSG00000187912), CLEC4C (ENSG00000198178), CLEC6A (ENSG00000205846)

Protein

Protein identifiers

C-type lectin domain family 10 member A — Q8IUN9 (reviewed: Q8IUN9)

Alternative names: C-type lectin superfamily member 14, DC-asialoglycoprotein receptor, Macrophage galactose-type lectin, Macrophage lectin 2

All UniProt accessions (3): Q8IUN9, I3NI09, J3KR22

UniProt curated annotations — full annotation on UniProt →

Function. C-type lectin receptor involved in recognition of N-acetylgalactosamine (GalNAc)-terminated glycans by myeloid antigen presenting cells (APCs). Binds in a Ca(2+)-dependent manner to alpha- and beta-linked GalNAc residues on glycoprotein and glycolipid antigens, including alphaGalNAc- and Galbeta1->3GalNAc-O-Ser/Thr also known as Tn and T antigens, LacdiNAc epitope GalNAcbeta1->4GlcNAc and its derivative GalNAcbeta1->4-(Fucalpha1->3)GlcNAc, O-linked core 5 and 6 glycans, and GM2 and GD2 gangliosides. Acts as a signaling receptor at the interface of APC-T cell interactions. On immature dendritic cells, recognizes Tn antigen-carrying PTPRC/CD45 receptor on effector T cells and downregulates PTRPN/CD45 phosphatase activity with an impact on T cell activation threshold, cytokine production and proliferation. Modulates dendritic cell maturation toward a tolerogenic phenotype leading to generation of regulatory CD4-positive T cell subset with immune suppressive functions. Acts as an endocytic pattern recognition receptor involved in antitumor immunity. During tumorigenesis, recognizes Tn antigens and its sialylated forms Neu5Ac-Tn and Neu5Gc-Tn expressed on tumor cell mucins. On immature dendritic cells, can internalize Tn-terminated immunogens and target them to endolysosomal compartment for MHC class I and II antigen presentation to CD8-positive and CD4-positive T cells, respectively.

Subunit / interactions. Interacts with A-, B- and C-domain containing PTPRC/CD45 isoforms: isoform 1/CD45ABC, isoform 3/CD45AB, isoform 5/CD45BC and isoform 7/CD45B. Does not interact with PTPRC/CD45 isoform 2/CD45RO, a memory T cell marker.

Subcellular location. Cell membrane. Early endosome membrane. Lysosome membrane.

Tissue specificity. Expressed in myeloid antigen presenting cells in lymph nodes and skin (at protein level). Expressed in dermal dendritic cells (at protein level).

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IUN9-1	1	yes
Q8IUN9-2	2
Q8IUN9-3	3

RefSeq proteins (3): NP_001316999, NP_006335, NP_878910 (=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, PF03954

UniProt features (50 total): binding site 17, strand 7, splice variant 4, sequence variant 4, disulfide bond 3, mutagenesis site 3, topological domain 2, glycosylation site 2, helix 2, chain 1, transmembrane region 1, domain 1, sequence conflict 1, coiled-coil region 1, short sequence motif 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
6PUV	X-RAY DIFFRACTION	1.2
6PY1	X-RAY DIFFRACTION	1.7
6W12	X-RAY DIFFRACTION	2
6XIY	X-RAY DIFFRACTION	2.31

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IUN9-F1	80.65	0.52

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 (17): 243; 267; 269; 269; 270; 280; 280; 280; 281; 286; 292; 292 …

Disulfide bonds (3): 181–192, 209–304, 282–296

Glycosylation sites (2): 78, 173

Mutagenesis-validated functional residues (3):

Position	Phenotype
5	loss of receptor-mediated endocytosis.
30	45% reduction of receptor-mediated endocytosis; when associated with a-31.
31	45% reduction of receptor-mediated endocytosis; when associated with a-30.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5621480	Dectin-2 family

MSigDB gene sets: 186 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, REACTOME_INNATE_IMMUNE_SYSTEM, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOCC_VACUOLAR_MEMBRANE, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOCC_CELL_SURFACE, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, MARTINEZ_RB1_TARGETS_DN, MODULE_410, GOBP_ADAPTIVE_IMMUNE_RESPONSE, NRF2_Q4, BROWN_MYELOID_CELL_DEVELOPMENT_DN, RYTTCCTG_ETS2_B, GOBP_IMPORT_INTO_CELL

GO Biological Process (5): adaptive immune response (GO:0002250), endocytosis (GO:0006897), immune response (GO:0006955), innate immune response (GO:0045087), immune system process (GO:0002376)

GO Molecular Function (5): D-mannose binding (GO:0005537), carbohydrate binding (GO:0030246), pattern recognition receptor activity (GO:0038187), fucose binding (GO:0042806), protein binding (GO:0005515)

GO Cellular Component (7): lysosomal membrane (GO:0005765), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), early endosome membrane (GO:0031901), lysosome (GO:0005764), endosome (GO:0005768), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
C-type lectin receptors (CLRs)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
immune response	2
monosaccharide binding	2
binding	2
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
immune system process	1
response to stimulus	1
defense response to symbiont	1
biological_process	1
signaling receptor activity	1
lysosome	1
lytic vacuole membrane	1
membrane	1
cell periphery	1
plasma membrane	1
cell surface	1
side of membrane	1
early endosome	1
endosome membrane	1
lytic vacuole	1
endomembrane system	1
cytoplasmic vesicle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1594 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC10A	LLGL1	Q15334	743
CLEC10A	ITGAX	P20702	714
CLEC10A	EEF1A2	P54266	705
CLEC10A	ITGAE	P38570	573
CLEC10A	CD1C	P29017	544
CLEC10A	IL2	P01585	529
CLEC10A	FCER1A	P12319	511
CLEC10A	CD163	Q86VB7	507
CLEC10A	MPPE1	Q53F39	505
CLEC10A	ITGAM	P11215	495
CLEC10A	ARG1	P05089	480
CLEC10A	IL10	P22301	476
CLEC10A	MUC1	P13931	464
CLEC10A	XCR1	P46094	464
CLEC10A	CLEC7A	Q9BXN2	463

IntAct

83 interactions, top by confidence:

A	B	Type	Score
CLEC10A	GIMAP1	psi-mi:“MI:0915”(physical association)	0.600
ZFPL1	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
TSPO	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
TUSC5	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
TMEM218	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	SLC38A7	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	PEX16	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	ZDHHC15	psi-mi:“MI:0915”(physical association)	0.560
VSTM1	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	SMCO4	psi-mi:“MI:0915”(physical association)	0.560
ADIPOQ	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	SEC22A	psi-mi:“MI:0915”(physical association)	0.560
PRAF2	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
APOD	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
MALL	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
BET1	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	CLN6	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	NAPB	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	FXYD6	psi-mi:“MI:0915”(physical association)	0.560
UNC50	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	ACSF2	psi-mi:“MI:0915”(physical association)	0.560
TNF	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
FMO3	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
TTMP	CLEC10A	psi-mi:“MI:0915”(physical association)	0.560
CLEC10A	FAM241A	psi-mi:“MI:0915”(physical association)	0.500
CLEC10A	S	psi-mi:“MI:0407”(direct interaction)	0.440
CFTR	CLEC10A	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (39): C4orf32 (Affinity Capture-MS), C4orf32 (Affinity Capture-MS), CST6 (Affinity Capture-MS), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), CLEC10A (Two-hybrid), FXYD6 (Two-hybrid)

ESM2 similar proteins: A4KWA1, O88200, O88201, P02706, P07306, P07307, P08290, P18519, P21854, P24721, P26951, P27471, P27812, P27814, P34927, P49300, P49301, P78380, P79391, Q0VCS6, Q2HXU8, Q3LUH2, Q3SXB8, Q49BZ4, Q5NKN2, Q5NKN4, Q5RBQ8, Q61190, Q6QLQ4, Q6UX15, Q6UXB4, Q8BNX1, Q8BWY2, Q8C1T8, Q8HZR8, Q8IUN9, Q8NC01, Q8VBX4, Q8VD98, Q8WTT0

Diamond homologs: A4KWA1, A4KWA5, A4KWA6, A4KWA8, O89335, P02706, P08290, P0C7M8, P0C7M9, P14371, P24721, P26715, P26717, P34927, P37217, Q07108, Q07444, Q0H8B9, Q0ZCA7, Q5M9I1, Q60660, Q6EIG7, Q6QLQ4, Q6UVW9, Q6UXN8, Q80XD9, Q8BWY2, Q8C1T8, Q8HY02, Q8HY10, Q8HY11, Q8HY12, Q8IUN9, Q8MIS5, Q8N1N0, Q8VI21, Q8WTT0, Q90WJ8, Q91V08, Q92478

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	29
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1364 predictions. Top by Δscore:

Variant	Effect	Δscore
17:7075358:A:AC	donor_gain	1.0000
17:7075359:C:CC	donor_gain	1.0000
17:7075725:CCTCA:C	donor_loss	1.0000
17:7075726:CTCA:C	donor_loss	1.0000
17:7075729:ACCTG:A	donor_loss	1.0000
17:7075730:CCTG:C	donor_gain	1.0000
17:7075730:CCTGC:C	donor_loss	1.0000
17:7075739:C:A	donor_gain	1.0000
17:7075881:GGAGG:G	acceptor_gain	1.0000
17:7075882:GAGG:G	acceptor_gain	1.0000
17:7075883:AGG:A	acceptor_gain	1.0000
17:7075883:AGGC:A	acceptor_loss	1.0000
17:7075884:GG:G	acceptor_gain	1.0000
17:7075885:GCTGA:G	acceptor_loss	1.0000
17:7075886:C:CC	acceptor_gain	1.0000
17:7075886:C:G	acceptor_loss	1.0000
17:7075890:T:C	acceptor_gain	1.0000
17:7075890:T:TC	acceptor_gain	1.0000
17:7076068:TGAA:T	acceptor_gain	1.0000
17:7076072:C:CC	acceptor_gain	1.0000
17:7076727:TCTCA:T	donor_loss	1.0000
17:7076728:CTCA:C	donor_loss	1.0000
17:7076729:TCA:T	donor_loss	1.0000
17:7076730:CAC:C	donor_loss	1.0000
17:7076731:A:AG	donor_loss	1.0000
17:7076801:CTGC:C	acceptor_gain	1.0000
17:7076802:TGC:T	acceptor_gain	1.0000
17:7076803:GC:G	acceptor_gain	1.0000
17:7076804:CC:C	acceptor_gain	1.0000
17:7076805:C:CC	acceptor_gain	1.0000

AlphaMissense

1907 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:7075216:C:A	W263C	0.998
17:7075216:C:G	W263C	0.998
17:7075132:C:A	W291C	0.997
17:7075132:C:G	W291C	0.997
17:7075392:C:A	W250C	0.997
17:7075392:C:G	W250C	0.997
17:7075134:A:G	W291R	0.994
17:7075134:A:T	W291R	0.994
17:7075398:C:A	W248C	0.993
17:7075398:C:G	W248C	0.993
17:7075428:C:A	W238C	0.992
17:7075428:C:G	W238C	0.992
17:7075218:A:G	W263R	0.991
17:7075218:A:T	W263R	0.991
17:7075394:A:G	W250R	0.990
17:7075394:A:T	W250R	0.990
17:7075166:T:A	E280V	0.989
17:7075793:C:G	A205P	0.989
17:7075160:C:G	C282S	0.988
17:7075161:A:T	C282S	0.988
17:7075851:C:A	W185C	0.988
17:7075851:C:G	W185C	0.988
17:7075800:C:A	W202C	0.987
17:7075800:C:G	W202C	0.987
17:7075129:A:C	N292K	0.986
17:7075129:A:T	N292K	0.986
17:7075780:C:G	C209S	0.986
17:7075781:A:T	C209S	0.986
17:7075094:C:G	C304S	0.985
17:7075095:A:T	C304S	0.985

dbSNP variants (sampled 300 via entrez): RS1000122706 (17:7077849 T>C), RS1000152392 (17:7078060 G>A), RS1000696172 (17:7079588 A>G), RS1000748691 (17:7079836 G>A), RS1001802485 (17:7078613 G>A,T), RS1002241318 (17:7080639 G>A,C), RS1002353862 (17:7074307 G>A), RS1002459084 (17:7081702 G>C), RS1002575031 (17:7081930 C>A,T), RS1002746538 (17:7076547 C>A,T), RS1003094045 (17:7075747 T>A,C), RS1003172117 (17:7081152 C>T), RS1003210384 (17:7076861 C>T), RS1004176841 (17:7079904 C>T), RS1004314105 (17:7080071 T>C,G)

Disease associations

OMIM: gene MIM:605999 | 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
GCST005166_3	GIP levels in response to oral glucose tolerance test (120 minutes)	1.000000e-06
GCST008478_42	Neurological blood protein biomarker levels	6.000000e-14
GCST008478_69	Neurological blood protein biomarker levels	2.000000e-12
GCST010151_25	Carotid intima media thickness x smoking interaction	4.000000e-06
GCST90013406_6	Liver enzyme levels (alkaline phosphatase)	1.000000e-300

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004307	glucose tolerance test
EFO:0008464	glucose-dependent insulinotropic peptide measurement
EFO:0006527	smoking status measurement
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Lipopolysaccharides	increases expression, affects cotreatment, decreases expression, decreases reaction	2
pirinixic acid	affects binding, decreases expression, increases activity	1
2,4,5,2’,4’,5’-hexachlorobiphenyl	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
bardoxolone methyl	decreases reaction, increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
gardiquimod	decreases expression, decreases reaction	1
Acetaminophen	decreases expression	1
Allergens	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Dietary Fats	increases expression, increases reaction	1
Nickel	increases expression	1
Valproic Acid	affects expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	increases expression	1
Protein Kinase Inhibitors	decreases expression, decreases reaction	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1CT	Ubigene THP-1 CLEC10A KO	Cancer cell line	Male

Clinical trials (associated diseases)

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