CCL13

Summary

CCL13 (C-C motif chemokine ligand 13, HGNC:10611) is a protein-coding gene on chromosome 17q12, encoding C-C motif chemokine 13 (Q99616). Chemotactic factor that attracts monocytes, lymphocytes, basophils and eosinophils, but not neutrophils.

This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for monocytes, lymphocytes, basophils and eosinophils, but not neutrophils. This chemokine plays a role in accumulation of leukocytes during inflammation. It may also be involved in the recruitment of monocytes into the arterial wall during artherosclerosis.

Source: NCBI Gene 6357 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_005408

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10611
Approved symbol	CCL13
Name	C-C motif chemokine ligand 13
Location	17q12
Locus type	gene with protein product
Status	Approved
Aliases	MCP-4, NCC-1, SCYL1, CKb10, MGC17134
Ensembl gene	ENSG00000181374
Ensembl biotype	protein_coding
OMIM	601391
Entrez	6357

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000225844, ENST00000577681

RefSeq mRNA: 1 — MANE Select: NM_005408 NM_005408

CCDS: CCDS11281

Canonical transcript exons

ENST00000225844 — 3 exons

Exon	Start	End
ENSE00000713749	34357475	34357589
ENSE00001243919	34358026	34358610
ENSE00001243928	34356480	34356602

Expression profiles

Bgee: expression breadth ubiquitous, 174 present calls, max score 92.99.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.7062 / max 748.8021, expressed in 124 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160319	1.5781	116
160318	0.1281	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.99	gold quality
mucosa of transverse colon	UBERON:0004991	90.31	gold quality
decidua	UBERON:0002450	88.76	gold quality
tibial nerve	UBERON:0001323	87.65	gold quality
colonic epithelium	UBERON:0000397	86.00	gold quality
tendon of biceps brachii	UBERON:0008188	83.79	gold quality
rectum	UBERON:0001052	83.59	gold quality
calcaneal tendon	UBERON:0003701	82.48	gold quality
duodenum	UBERON:0002114	82.08	gold quality
transverse colon	UBERON:0001157	81.56	gold quality
right adrenal gland cortex	UBERON:0035827	81.26	gold quality
upper leg skin	UBERON:0004262	81.08	gold quality
tendon	UBERON:0000043	80.90	gold quality
upper arm skin	UBERON:0004263	80.86	silver quality
upper lobe of left lung	UBERON:0008952	80.21	gold quality
small intestine Peyer’s patch	UBERON:0003454	80.08	gold quality
small intestine	UBERON:0002108	79.46	gold quality
upper lobe of lung	UBERON:0008948	79.18	gold quality
smooth muscle tissue	UBERON:0001135	77.61	gold quality
layer of synovial tissue	UBERON:0007616	77.47	gold quality
left coronary artery	UBERON:0001626	77.27	gold quality
coronary artery	UBERON:0001621	76.46	gold quality
synovial joint	UBERON:0002217	75.49	gold quality
caecum	UBERON:0001153	75.45	gold quality
right coronary artery	UBERON:0001625	75.41	gold quality
right adrenal gland	UBERON:0001233	75.17	gold quality
subcutaneous adipose tissue	UBERON:0002190	74.92	gold quality
lung	UBERON:0002048	74.57	gold quality
left adrenal gland	UBERON:0001234	74.33	gold quality
adrenal cortex	UBERON:0001235	74.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.73

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): BCL6, NFKB1, NFKB, RELA, STAT6, TFAP2A, YY1

miRNA regulators (miRDB)

25 targeting CCL13, 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-3667-3P	99.99	67.17	1636
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-2276-3P	98.76	67.75	1384
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-3145-5P	98.57	67.83	900
HSA-MIR-4662A-5P	98.48	67.18	1007
HSA-MIR-224-5P	98.33	70.12	1256
HSA-MIR-4660	97.79	67.44	1328
HSA-MIR-634	97.74	67.11	818
HSA-MIR-324-5P	95.68	65.20	560

Literature-anchored findings (GeneRIF, showing 23)

• Data suggest that the monocyte chemoattractant protein-4 core promoter YY-1 binding motif is functional, and modulates the transcriptional regulation of the MCP-4 gene. (PMID:12805085)
• CCL13 is an antimicrobial protein with bacteriocidal activity against E. coli. (PMID:12949249)
• The study was undertaken to understand the relationship between the functional proteomics of receptor-Ck and developmental stages of human atherosclerotic aortic wall. (PMID:14560935)
• MCP-4 may be a critical molecule that links obesity and chronic inflammation. (PMID:16855189)
• Differential transcription occurring early in atopic dermatitis skin was indicated for CCL18, CCL13, IFNalpha2, PPARalpha and PPARgamma. (PMID:17181634)
• The Th2 cytokine IL-4 preferentially stimulated MCP-4 expression. (PMID:17541284)
• interferon-gamma with IL-1beta/TNF-alpha activates the production of CCL13 from chondrocytes in RA joints; secreted CCL13 enhances fibroblast-like synoviocyte proliferation by activating the extracellular signal-regulated MAP kinases cascade (PMID:17824960)
• TLR2, 3, 4 and 5 ligands, but not TLR7/8 or 9 ligands, synergized with IL-4 to induce the production of MCP-4 in nasal polyp fibroblasts. (PMID:17851891)
• CCL13 and HSPC159 mRNA expressions in PBMC are up-regulated specifically in MCNS patients during the nephrosis phase. (PMID:18219197)
• MMP-12 truncates and inactivates ELR+ CXC chemokines and generates CCL2, -7, -8, and -13 antagonists (PMID:18660381)
• Oncostatin M can strongly up-regulate the expression of CCL13, a chemokine recently identified in the synovial fluid of patients with rheumatoid arthritis. (PMID:19565514)
• Findings suggest that the pro-atherogenic effects of CCR2 may not be restricted to interaction with MCP-1, but could also involve activation by MCP-4, being an inflammatory link between platelet and monocyte activation. (PMID:20139115)
• Data show that, for the small macrophages in COPD, increased transcript and protein levels for CCL2, CCL7, CCL13 and CCL22 with a more than 100-fold increase for CCL13 mRNA. (PMID:21327296)
• E(2) has adverse effects on the pathogenesis of RA as a result of unregulated cell death, increased TNF-alpha-induced MMP-3 production, and CCL13 overproduction, subsequently resulting in the disease progression of RA. (PMID:22393877)
• MCP-4 and hsCRP may be the markers linking chronic inflammation in obesity and periodontal disease. (PMID:23375121)
• Data suggest that CCL13 binds to several chemokine receptors (CCR1, CCR2, and CCR3), allowing CCL13 to elicit different effects on target cells of immune system. CCL13 is involved in pathology of chronic inflammatory/autoimmune diseases. [REVIEW] (PMID:23846739)
• identified 13 ADCC-activated genes. Six gene expression assays including 8 of the 13 genes (CCL3, CCL4/CCL4L1/CCL4L2, CD160, IFNG, NR4A3 and XCL1/XCL2) were analyzed in 127 kidney biopsies (PMID:25449536)
• CCL13 levels in serum and synovial fluid may serve as a biomarker for the progression of osteoarthritis. (PMID:25654294)
• The reduction of circulating levels of MCP-4, eotaxin-3, and MIP-1beta could be one of the mechanisms by which bariatric surgery contributes to the reduction of cardiovascular risk in these patients. (PMID:27300476)
• CCL13 expression is significantly upregulated in human masticatory mucosa during wound healing (PMID:28005267)
• In plasma, but not CSF, the bivariate MCP4 (CCL13)/ MCP1(CCL2) ratio is ca. twofold elevated in PTSD patients compared with healthy controls. (PMID:28170001)
• CCL13 and human diseases. (PMID:37153575)
• MCP-4 and Eotaxin-3 Are Novel Biomarkers for Chronic Obstructive Pulmonary Disease. (PMID:37200921)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	cxcl32b.1	ENSDARG00000071499

Paralogs (26): CX3CL1 (ENSG00000006210), CCL26 (ENSG00000006606), CCL22 (ENSG00000102962), CCL17 (ENSG00000102970), CCL24 (ENSG00000106178), CCL7 (ENSG00000108688), CCL2 (ENSG00000108691), CCL8 (ENSG00000108700), CCL1 (ENSG00000108702), CCL20 (ENSG00000115009), CCL25 (ENSG00000131142), CCL21 (ENSG00000137077), XCL1 (ENSG00000143184), XCL2 (ENSG00000143185), CCL11 (ENSG00000172156), CCL19 (ENSG00000172724), CCL5 (ENSG00000271503), CCL23 (ENSG00000274736), CCL16 (ENSG00000275152), CCL4 (ENSG00000275302), CCL18 (ENSG00000275385), CCL15 (ENSG00000275718), CCL4L2 (ENSG00000276070), CCL3L3 (ENSG00000276085), CCL14 (ENSG00000276409), CCL3 (ENSG00000277632)

Protein

Protein identifiers

C-C motif chemokine 13 — Q99616 (reviewed: Q99616)

Alternative names: CK-beta-10, Monocyte chemoattractant protein 4, Monocyte chemotactic protein 4, NCC-1, Small-inducible cytokine A13

All UniProt accessions (2): Q99616, J3QLQ9

UniProt curated annotations — full annotation on UniProt →

Function. Chemotactic factor that attracts monocytes, lymphocytes, basophils and eosinophils, but not neutrophils. Signals through CCR2B and CCR3 receptors. Plays a role in the accumulation of leukocytes at both sides of allergic and non-allergic inflammation. May be involved in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis. May play a role in the monocyte attraction in tissues chronically exposed to exogenous pathogens.

Subcellular location. Secreted.

Tissue specificity. Widely expressed. Found in small intestine, thymus, colon, lung, trachea, stomach and lymph node. Low levels seen in the pulmonary artery smooth muscle cells.

Post-translational modifications. One major form (form long), and two minor forms (short chain and medium chain) are produced by differential signal peptide cleavage. The medium chain is about 30-fold less active than the long chain.

Induction. By IL1/interleukin-1 and TNF.

Miscellaneous. This protein can bind heparin.

Similarity. Belongs to the intercrine beta (chemokine CC) family.

RefSeq proteins (1): NP_005399* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000827	Chemokine_CC_CS	Conserved_site
IPR001811	Chemokine_IL8-like_dom	Domain
IPR036048	Interleukin_8-like_sf	Homologous_superfamily
IPR039809	Chemokine_b/g/d	Family

Pfam: PF00048

UniProt features (17 total): strand 5, chain 3, helix 2, disulfide bond 2, sequence variant 2, signal peptide 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2RA4	X-RAY DIFFRACTION	1.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99616-F1	85.39	0.61

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): 24

Disulfide bonds (2): 34–58, 35–74

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

ID	Pathway
R-HSA-380108	Chemokine receptors bind chemokines
R-HSA-418594	G alpha (i) signalling events
R-HSA-162582	Signal Transduction
R-HSA-372790	Signaling by GPCR
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)
R-HSA-375276	Peptide ligand-binding receptors
R-HSA-388396	GPCR downstream signalling
R-HSA-500792	GPCR ligand binding

MSigDB gene sets: 230 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, MODULE_92, GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_MYELOID_LEUKOCYTE_MIGRATION, GOBP_CELL_CHEMOTAXIS, GOBP_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_PEPTIDE, MODULE_64, GAURNIER_PSMD4_TARGETS, GOBP_CELL_CELL_SIGNALING, GOBP_LEUKOCYTE_CHEMOTAXIS, GOBP_TAXIS, GOBP_LEUKOCYTE_MIGRATION, REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS

GO Biological Process (14): intracellular calcium ion homeostasis (GO:0006874), chemotaxis (GO:0006935), inflammatory response (GO:0006954), cytoskeleton organization (GO:0007010), signal transduction (GO:0007165), cell-cell signaling (GO:0007267), regulation of cell shape (GO:0008360), positive regulation of cell migration (GO:0030335), killing of cells of another organism (GO:0031640), eosinophil chemotaxis (GO:0048245), antimicrobial humoral immune response mediated by antimicrobial peptide (GO:0061844), chemokine-mediated signaling pathway (GO:0070098), immune response (GO:0006955), cell chemotaxis (GO:0060326)

GO Molecular Function (5): signaling receptor binding (GO:0005102), chemokine activity (GO:0008009), CCR chemokine receptor binding (GO:0048020), cytokine activity (GO:0005125), protein binding (GO:0005515)

GO Cellular Component (2): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Signaling by GPCR	2
Peptide ligand-binding receptors	1
GPCR downstream signalling	1
Signal Transduction	1
GPCR ligand binding	1
Class A/1 (Rhodopsin-like receptors)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell communication	2
signaling	2
cell migration	2
chemokine receptor binding	2
intracellular monoatomic cation homeostasis	1
calcium ion homeostasis	1
response to chemical	1
taxis	1
defense response	1
organelle organization	1
cellular process	1
regulation of cellular process	1
cellular response to stimulus	1
regulation of cell morphogenesis	1
regulation of biological quality	1
regulation of cell migration	1
positive regulation of cell motility	1
cell killing	1
disruption of cell in another organism	1
granulocyte chemotaxis	1
eosinophil migration	1
antimicrobial humoral response	1
G protein-coupled receptor signaling pathway	1
cytokine-mediated signaling pathway	1
cellular response to chemokine	1
immune system process	1
response to stimulus	1
chemotaxis	1
cellular response to chemical stimulus	1
protein binding	1
cytokine activity	1
cell chemotaxis	1
receptor ligand activity	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1155 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCL13	CCR3	P51677	995
CCL13	CCR2	P41597	992
CCL13	CCR1	P32246	990
CCL13	CCR5	P51681	985
CCL13	ACKR2	O00590	855
CCL13	A0A0J9YW77	A0A0J9YW77	827
CCL13	CXCL6	P80162	759
CCL13	CCL2	P13500	756
CCL13	IL1B	P01584	734
CCL13	CCL25	O15444	733
CCL13	CXCL13	O43927	722
CCL13	IL10	P22301	696
CCL13	CCL19	Q99731	693
CCL13	CXCL10	P02778	679
CCL13	ACKR4	Q9NPB9	651

IntAct

28 interactions, top by confidence:

A	B	Type	Score
CCL13	CCL5	psi-mi:“MI:0407”(direct interaction)	0.560
CCL13	PF4	psi-mi:“MI:0407”(direct interaction)	0.560
CCL13	CXCL12	psi-mi:“MI:0407”(direct interaction)	0.560
CCL5	CCL13	psi-mi:“MI:0407”(direct interaction)	0.560
PF4	CCL13	psi-mi:“MI:0407”(direct interaction)	0.560
CCL13	CCL8	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	CCL11	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	CCL21	psi-mi:“MI:0407”(direct interaction)	0.440
CCL26	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
CCL28	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
XCL1	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
PPBP	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
CXCL9	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
CXCL10	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
CXCL11	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
CXCL14	CCL13	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	CCL24	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	CCL26	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	XCL1	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	CXCL10	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	CXCL11	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	CXCL17	psi-mi:“MI:0407”(direct interaction)	0.440
CCL13	NPM1	psi-mi:“MI:0915”(physical association)	0.400
HNRNPH3	CCL13	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (28): CCL13 (Two-hybrid), CCL13 (Proximity Label-MS), CCL11 (Reconstituted Complex), CCL2 (Reconstituted Complex), CCL21 (Reconstituted Complex), CCL24 (Reconstituted Complex), CCL26 (Reconstituted Complex), CCL28 (Reconstituted Complex), CCL5 (Reconstituted Complex), CCL8 (Reconstituted Complex), CXCL10 (Reconstituted Complex), CXCL11 (Reconstituted Complex), CXCL12 (Reconstituted Complex), CXCL17 (Reconstituted Complex), XCL1 (Reconstituted Complex)

ESM2 similar proteins: A9QWQ1, O14625, O46675, O46676, O46677, O46678, O89098, O97919, P08317, P09340, P09341, P10147, P10855, P10889, P12850, P13236, P13501, P14095, P14097, P16619, P19875, P19876, P30782, P30882, P42831, P46632, P47854, P50229, P50230, P50231, P97272, Q17QA1, Q5EBF6, Q5I1Z0, Q5RA36, Q68A92, Q68AZ0, Q711P4, Q8HYQ1, Q8HYQ2

Diamond homologs: F5HET8, O00175, O00585, O00626, O55145, O88430, O97919, P10147, P10148, P10855, P13236, P13500, P13501, P14097, P14844, P16619, P27784, P28291, P28292, P30882, P42831, P46632, P47993, P49873, P50229, P50230, P50231, P51670, P51671, P52203, P55773, P55774, P61274, P61275, P78423, P80075, P80098, P80343, P82943, P97272

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 18 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Chemokine receptors bind chemokines	11	171.6×	2e-23
Class A/1 (Rhodopsin-like receptors)	5	30.9×	3e-06
Peptide ligand-binding receptors	5	30.9×	3e-06
G alpha (i) signalling events	9	29.2×	2e-11
GPCR ligand binding	5	26.7×	5e-06
Signaling by GPCR	5	16.7×	4e-05

GO biological processes:

GO term	Partners	Fold	FDR
eosinophil chemotaxis	6	244.2×	2e-12
chemokine-mediated signaling pathway	12	216.1×	9e-25
neutrophil chemotaxis	7	111.1×	5e-12
antimicrobial humoral immune response mediated by antimicrobial peptide	11	99.0×	1e-18
chemotaxis	11	83.0×	6e-18
cell chemotaxis	7	72.0×	1e-10
response to virus	5	40.0×	2e-06
cell-cell signaling	10	38.7×	6e-13

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3165 predictions. Top by Δscore:

Variant	Effect	Δscore
11:65525261:GAAG:G	donor_gain	1.0000
11:65525262:AAGG:A	donor_loss	1.0000
11:65525263:AGGTG:A	donor_loss	1.0000
11:65525264:GGT:G	donor_loss	1.0000
11:65525265:G:A	donor_loss	1.0000
11:65525265:G:GG	donor_gain	1.0000
11:65525266:T:A	donor_loss	1.0000
11:65525569:CCTA:C	acceptor_loss	1.0000
11:65525570:CTA:C	acceptor_loss	1.0000
11:65525571:TA:T	acceptor_loss	1.0000
11:65525573:G:A	acceptor_loss	1.0000
11:65525712:G:GT	donor_gain	1.0000
11:65525714:GGTA:G	donor_loss	1.0000
11:65525716:T:G	donor_loss	1.0000
11:65525915:CCCCA:C	acceptor_loss	1.0000
11:65525916:CCCAG:C	acceptor_loss	1.0000
11:65525917:CCAG:C	acceptor_loss	1.0000
11:65525918:CAG:C	acceptor_loss	1.0000
11:65525919:A:AG	acceptor_gain	1.0000
11:65525919:AGA:A	acceptor_loss	1.0000
11:65525920:G:A	acceptor_loss	1.0000
11:65525920:G:GG	acceptor_gain	1.0000
11:65525920:GACA:G	acceptor_gain	1.0000
11:65526123:GAAA:G	acceptor_gain	1.0000
11:65526213:G:GT	donor_gain	1.0000
11:65526294:GCA:G	donor_gain	1.0000
11:65526297:G:GG	donor_gain	1.0000
11:65526348:GTG:G	donor_gain	1.0000
11:65526956:CTACA:C	acceptor_loss	1.0000
11:65526957:TACAG:T	acceptor_loss	1.0000

AlphaMissense

640 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:34358077:G:C	W81C	0.966
17:34358077:G:T	W81C	0.966
17:34358028:T:C	F65S	0.940
17:34358075:T:A	W81R	0.908
17:34358075:T:C	W81R	0.908
17:34358028:T:G	F65C	0.907
17:34357586:T:A	V63D	0.902
17:34357570:T:C	C58R	0.875
17:34357570:T:A	C58S	0.873
17:34357571:G:C	C58S	0.873
17:34358079:T:A	V82D	0.851
17:34358027:T:C	F65L	0.849
17:34358029:C:A	F65L	0.849
17:34358029:C:G	F65L	0.849
17:34358054:T:A	C74S	0.842
17:34358055:G:C	C74S	0.842
17:34357501:T:A	C35S	0.819
17:34357502:G:C	C35S	0.819
17:34358057:G:C	A75P	0.819
17:34357541:T:C	L48P	0.812
17:34357504:T:C	F36L	0.800
17:34357506:C:A	F36L	0.800
17:34357506:C:G	F36L	0.800
17:34358078:G:C	V82L	0.796
17:34358056:T:G	C74W	0.793
17:34358054:T:C	C74R	0.792
17:34357501:T:C	C35R	0.786
17:34357503:C:G	C35W	0.779
17:34358058:C:A	A75D	0.771
17:34357498:T:C	C34R	0.762

dbSNP variants (sampled 300 via entrez): RS1000044301 (17:34355853 C>A), RS1000171134 (17:34358866 C>A,T), RS1000544315 (17:34359064 T>C), RS1001689599 (17:34354628 G>T), RS1002182252 (17:34356528 T>A,C), RS1002926208 (17:34355138 T>A), RS1003827321 (17:34355565 G>A), RS1004194709 (17:34356926 C>A,T), RS1004283448 (17:34358890 C>A,T), RS1004529614 (17:34355827 T>C), RS1005020925 (17:34357767 A>G), RS1006586914 (17:34355484 T>C), RS1006698136 (17:34358580 G>T), RS1007050322 (17:34355232 C>T), RS1008402316 (17:34357021 G>T)

Disease associations

OMIM: gene MIM:601391 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001438_14	Crohn’s disease	4.000000e-08
GCST001725_28	Inflammatory bowel disease	1.000000e-26
GCST009391_1216	Metabolite levels	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010420	triacylglycerol 54:2 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, decreases methylation, increases methylation	2
Nickel	increases expression	2
bisphenol A	increases expression	1
sodium arsenite	decreases expression	1
nickel sulfate	decreases expression	1
2,4-dinitrofluorobenzene sulfonic acid	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Troglitazone	decreases expression	1
Calcium	increases uptake	1
Dexamethasone	affects cotreatment, decreases expression	1
Estradiol	affects expression, increases expression	1
Eugenol	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Latex	increases expression	1
Methotrexate	decreases expression	1
Perfume	increases expression	1
Prednisone	decreases expression	1
Fenofibrate	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Mifepristone	decreases expression	1
Antirheumatic Agents	decreases expression	1
Nanotubes, Carbon	increases expression	1

Clinical trials (associated diseases)

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