EDIL3

Summary

EDIL3 (EGF like and discoidin domains 3, HGNC:3173) is a protein-coding gene on chromosome 5q14.3, encoding EGF-like repeat and discoidin I-like domain-containing protein 3 (O43854). Promotes adhesion of endothelial cells through interaction with the alpha-v/beta-3 integrin receptor.

The protein encoded by this gene is an integrin ligand. It plays an important role in mediating angiogenesis and may be important in vessel wall remodeling and development. It also influences endothelial cell behavior.

Source: NCBI Gene 10085 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 97 total
• MANE Select transcript: NM_005711

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3173
Approved symbol	EDIL3
Name	EGF like and discoidin domains 3
Location	5q14.3
Locus type	gene with protein product
Status	Approved
Aliases	DEL1
Ensembl gene	ENSG00000164176
Ensembl biotype	protein_coding
OMIM	606018
Entrez	10085

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000296591, ENST00000380138, ENST00000507663, ENST00000510271, ENST00000866584, ENST00000866585, ENST00000866586, ENST00000866587, ENST00000866588, ENST00000866589, ENST00000866590, ENST00000866591

RefSeq mRNA: 2 — MANE Select: NM_005711 NM_001278642, NM_005711

CCDS: CCDS4062, CCDS64195

Canonical transcript exons

ENST00000296591 — 11 exons

Exon	Start	End
ENSE00001082133	84254084	84254212
ENSE00001082136	84229855	84229884
ENSE00001127506	83963205	83963360
ENSE00001127541	84106649	84106830
ENSE00001235845	84384308	84384880
ENSE00001910544	83940554	83943568
ENSE00003471337	84060300	84060484
ENSE00003507146	84180393	84180521
ENSE00003510983	84137241	84137354
ENSE00003660674	84064700	84064844
ENSE00003679282	84066451	84066606

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 99.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 44.7868 / max 1162.6089, expressed in 1214 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
62389	13.9691	1042
62386	11.6306	1005
62380	5.6898	960
62388	3.8997	844
62379	3.8937	892
62382	2.3553	747
62384	1.1507	579
62387	0.9934	473
62385	0.5257	341
62383	0.3703	213

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lateral globus pallidus	UBERON:0002476	99.83	gold quality
inferior vagus X ganglion	UBERON:0005363	99.82	gold quality
substantia nigra pars reticulata	UBERON:0001966	99.81	gold quality
subthalamic nucleus	UBERON:0001906	99.80	gold quality
tibia	UBERON:0000979	99.74	gold quality
substantia nigra pars compacta	UBERON:0001965	99.64	gold quality
superior vestibular nucleus	UBERON:0007227	99.64	gold quality
pons	UBERON:0000988	99.63	gold quality
lateral nuclear group of thalamus	UBERON:0002736	99.51	gold quality
globus pallidus	UBERON:0001875	99.49	gold quality
ventral tegmental area	UBERON:0002691	99.48	gold quality
medial globus pallidus	UBERON:0002477	99.40	gold quality
postcentral gyrus	UBERON:0002581	99.35	gold quality
parietal lobe	UBERON:0001872	99.31	gold quality
trigeminal ganglion	UBERON:0001675	99.28	gold quality
corpus callosum	UBERON:0002336	99.21	gold quality
cartilage tissue	UBERON:0002418	98.97	gold quality
saphenous vein	UBERON:0007318	98.90	gold quality
corpus epididymis	UBERON:0004359	98.75	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.69	gold quality
entorhinal cortex	UBERON:0002728	98.60	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.59	gold quality
urethra	UBERON:0000057	98.29	gold quality
dorsal root ganglion	UBERON:0000044	98.28	gold quality
adult organism	UBERON:0007023	98.22	gold quality
vena cava	UBERON:0004087	98.17	gold quality
right coronary artery	UBERON:0001625	98.04	gold quality
spinal cord	UBERON:0002240	97.95	gold quality
stromal cell of endometrium	CL:0002255	97.65	gold quality
pigmented layer of retina	UBERON:0001782	97.60	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	120.57
E-HCAD-25	yes	64.00
E-MTAB-7316	yes	39.75
E-CURD-46	yes	29.56
E-GEOD-84465	yes	25.06
E-GEOD-137537	yes	14.25
E-CURD-119	yes	10.64
E-CURD-112	yes	8.22
E-HCAD-11	yes	6.34
E-ANND-3	yes	5.69
E-MTAB-7249	yes	2.99
E-GEOD-109979	no	184.25

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

222 targeting EDIL3, 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-3163	100.00	77.23	8605
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
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-507	99.97	70.11	1915
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-590-3P	99.96	74.34	6478

Literature-anchored findings (GeneRIF, showing 38)

• Del1 mediates vascular smooth muscle cell adhesion, migration, and proliferation through interaction with integrin alpha(v)beta(3). (PMID:11959660)
• acts as an angiogenic factor in the context of solid tumor formation; the increase in vascularization accelerates tumor growth through decreased apoptosis (PMID:12074641)
• Alpha v beta 5, alpha v beta 5 and their ligands Del-1 and L1 play an important role in the process of tumor cells moving from the original place. (PMID:18090124)
• Downregulation of developmentally regulated endothelial cell locus-1 inhibits the growth of colon cancer. (PMID:19292890)
• High expression level of EDIL3 predicts poor prognosis of hepatocellular carcinoma patients. (PMID:20857535)
• Del-1 mediates phosphatidylserine- and integrin-dependent endothelial uptake of microparticles by endocytosis. (PMID:22388320)
• database search for EGF domain sequences shows that this RGD finger is likely an evolutionary insertion and unique to the EGF domain of Del-1 (PMID:22601780)
• Del-1 may act as a gatekeeper of adrenal gland inflammation and may regulate the integrity of the hypothalamic-pituitary-adrenal axis stress response, thereby modulating adrenal (dys)function in the course of SIRS. (PMID:23364949)
• The reciprocal regulation between Del-1 and inflammation may contribute to optimally balance the protective and the potentially harmful effects of inflammatory cell recruitment. (PMID:24416060)
• The importance of interaction between EDIL3 and integrin alphaV. (PMID:25273699)
• Overexpression of the Del-1 gene potentiates proliferation and invasion of lung carcinoma cells. (PMID:26545781)
• Del-1 on circulating EVs is a promising marker to improve identification of patients with early-stage breast cancer and distinguish breast cancer from benign breast tumors and noncancerous diseases. (PMID:26603257)
• Del-1 pre-treatment of blood before addition of islets diminished coagulation activation and islet damage (PMID:26676803)
• Overexpressed EDIL3 promotes anchorage-independent tumor growth in human pancreatic cancer. (PMID:26735172)
• these data reveal an unrecognised function of endogenous Del-1 as a local inhibitor of ischaemia-induced angiogenesis by restraining LFA-1-dependent homing of pro-angiogenic haematopoietic cells to ischaemic tissues (PMID:28447099)
• EDIL3 may be implicated in retinal neovascularization in vitro. Silencing EDIL3 expression was demonstrated to impair the proliferative, migratory and tube forming capabilities of HRECs in vitro. (PMID:28765888)
• EDIL3 is significantly correlated with mesenchymal phenotype, angiogenesis, and tumor progression in lung adenocarcinoma. (PMID:28819306)
• Del-1-induced HSC proliferation and myeloid lineage commitment were mediated by beta3 integrin on hematopoietic progenitors. (PMID:28846069)
• these data demonstrate that Del-1 can negatively regulate IL-17 and its proinflammatory function, thereby limiting airway inflammation in allergic asthmatics, and suggest Del-1 as a potential candidate for prevention and treatment of allergic asthma. (PMID:29437247)
• protects chondrocytes from apoptosis (PMID:30278915)
• this study shows that DEL-1 promotes macrophage efferocytosis and clearance of inflammation (PMID:30455459)
• TAM-R breast cancer is characterized by Del-1 overexpression and tumor progression can be inhibited by Del-1 depletion, which restores TAM sensitivity. Thus, therapeutic strategies that target Del-1 may be effective for the treatment of hormone-resistant breast cancer. (PMID:31330520)
• Serum developmental endothelial locus-1 is associated with severity of sepsis in animals and humans. (PMID:31506547)
• Del-1, an Endogenous Inhibitor of TGF-beta Activation, Attenuates Fibrosis. (PMID:32117240)
• Psoriasis-associated angiogenesis is mediated by EDIL3. (PMID:32795468)
• The DEL-1/beta3 integrin axis promotes regulatory T cell responses during inflammation resolution. (PMID:32817592)
• Clinically confirmed DEL-1 as a myokine attenuates lipid-induced inflammation and insulin resistance in 3T3-L1 adipocytes via AMPK/HO-1- pathway. (PMID:32954935)
• Identification of a novel non-invasive biological marker to overcome the shortcomings of PSA in diagnosis and risk stratification for prostate cancer: Initial prospective study of developmental endothelial locus-1 protein. (PMID:33901217)
• Regulatory role of local tissue signal Del-1 in cancer and inflammation: a review. (PMID:34217213)
• Del-1 in Psoriasis Induced the Expression of alphavbeta3 and alpha5beta1 in Endothelial Cells. (PMID:34325631)
• Obesity and altered angiogenic-related gene expression in endometrial cancer. (PMID:34538531)
• Del1 Is a Growth Factor for Skeletal Progenitor Cells in the Fracture Callus. (PMID:37627279)
• An IL-10/DEL-1 axis supports granulopoiesis and survival from sepsis in early life. (PMID:38263289)
• Exploration of MELK as a downstream of Del-1 and druggable targets in triple-negative breast cancer. (PMID:38279017)
• Del-1 Plays a Protective Role against COPD Development by Inhibiting Inflammation and Apoptosis. (PMID:38396634)
• Epidermal Growth Factor-Like Repeats and Discoidin I-Like Domains 3 Deficiency Attenuates Dilated Cardiomyopathy by Inhibiting Ubiquitin Specific Peptidase 10 Dependent Smad4 Deubiquitination. (PMID:38456416)
• In silico analysis of DEL-1 and inflammation-related genes in lung squamous cell carcinoma. (PMID:39089131)
• Analysis of ANO6, HAPLN1, and EDIL3 Polymorphisms in Patients with Ankylosing Spondylitis in a Chinese Han Population: A Case-Control Study. (PMID:39358671)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	edil3b	ENSDARG00000060877
danio_rerio	edil3a	ENSDARG00000093413
mus_musculus	Edil3	ENSMUSG00000034488
rattus_norvegicus	Edil3	ENSRNOG00000033064

Paralogs (35): NRXN3 (ENSG00000021645), TLL1 (ENSG00000038295), CP (ENSG00000047457), DCBLD2 (ENSG00000057019), HEPH (ENSG00000089472), TLL2 (ENSG00000095587), NRP1 (ENSG00000099250), PCOLCE (ENSG00000106333), CNTNAP3 (ENSG00000106714), CUBN (ENSG00000107611), CNTNAP1 (ENSG00000108797), NRXN2 (ENSG00000110076), MEP1A (ENSG00000112818), NRP2 (ENSG00000118257), CUZD1 (ENSG00000138161), MFGE8 (ENSG00000140545), MEP1B (ENSG00000141434), PDGFC (ENSG00000145431), CNTNAP4 (ENSG00000152910), CNTNAP3B (ENSG00000154529), CNTNAP5 (ENSG00000155052), CDCP2 (ENSG00000157211), PCOLCE2 (ENSG00000163710), NETO1 (ENSG00000166342), BMP1 (ENSG00000168487), PDGFD (ENSG00000170962), NETO2 (ENSG00000171208), CNTNAP2 (ENSG00000174469), NRXN1 (ENSG00000179915), HEPHL1 (ENSG00000181333), F8 (ENSG00000185010), ASTL (ENSG00000188886), F5 (ENSG00000198734), MFRP (ENSG00000235718), CNTNAP3C (ENSG00000283378)

Protein

Protein identifiers

EGF-like repeat and discoidin I-like domain-containing protein 3 — O43854 (reviewed: O43854)

Alternative names: Developmentally-regulated endothelial cell locus 1 protein, Integrin-binding protein DEL1

All UniProt accessions (1): O43854

UniProt curated annotations — full annotation on UniProt →

Function. Promotes adhesion of endothelial cells through interaction with the alpha-v/beta-3 integrin receptor. Inhibits formation of vascular-like structures. May be involved in regulation of vascular morphogenesis of remodeling in embryonic development.

Subcellular location. Secreted.

Domain organisation. EGF2 and EGF3 form a rigid rod via an interdomain calcium ion binding site, while the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1.

Isoforms (2)

UniProt ID	Names	Canonical?
O43854-1	1, Long	yes
O43854-2	2, Short, Z20

RefSeq proteins (2): NP_001265571, NP_005702* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000152	EGF-type_Asp/Asn_hydroxyl_site	PTM
IPR000421	FA58C	Domain
IPR000742	EGF	Domain
IPR001881	EGF-like_Ca-bd_dom	Domain
IPR008979	Galactose-bd-like_sf	Homologous_superfamily
IPR013032	EGF-like_CS	Conserved_site
IPR018097	EGF_Ca-bd_CS	Conserved_site
IPR050633	Neuropilin_MCO_CoagFactor	Family

Pfam: PF00008, PF00754, PF12661

UniProt features (42 total): disulfide bond 12, strand 7, binding site 5, domain 5, glycosylation site 3, turn 3, splice variant 2, signal peptide 1, chain 1, sequence conflict 1, helix 1, short sequence motif 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4D90	X-RAY DIFFRACTION	2.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43854-F1	88.04	0.69

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 (5): 122; 136; 137; 119; 120

Disulfide bonds (12): 26–37, 31–48, 50–59, 78–89, 83–105, 107–116, 123–134, 128–143, 145–154, 158–314, 301–305, 319–476

Glycosylation sites (3): 73, 88, 140

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9926550	Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition

MSigDB gene sets: 234 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, RRAGTTGT_UNKNOWN, KOBAYASHI_EGFR_SIGNALING_24HR_UP, LIEN_BREAST_CARCINOMA_METAPLASTIC, MORF_RAD51L3, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP, WANG_RESPONSE_TO_BEXAROTENE_DN, MORF_CTSB, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT

GO Biological Process (2): cell adhesion (GO:0007155), positive regulation of cell-substrate adhesion (GO:0010811)

GO Molecular Function (4): integrin binding (GO:0005178), calcium ion binding (GO:0005509), extracellular matrix structural constituent (GO:0005201), metal ion binding (GO:0046872)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), extracellular matrix (GO:0031012), extracellular exosome (GO:0070062), extracellular vesicle (GO:1903561)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
MITF-M-dependent gene expression	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	1
regulation of cell-substrate adhesion	1
cell-substrate adhesion	1
positive regulation of cell adhesion	1
signaling receptor binding	1
protein-containing complex binding	1
cell adhesion molecule binding	1
metal ion binding	1
structural molecule activity	1
extracellular matrix	1
cation binding	1
cellular anatomical structure	1
external encapsulating structure	1
extracellular vesicle	1
extracellular region	1
vesicle	1
extracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1855 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EDIL3	HAPLN1	P10915	644
EDIL3	HOXD3	P31249	572
EDIL3	VTN	P01141	562
EDIL3	EGF	P01133	558
EDIL3	ITGAV	P06756	502
EDIL3	TP53	P04637	490
EDIL3	ITGB2	P05107	480
EDIL3	ITGB3	P05106	479
EDIL3	COL11A1	P12107	457
EDIL3	ZNF814	B7Z6K7	441
EDIL3	MEF2C	Q06413	435
EDIL3	PRDM5	Q9NQX1	433
EDIL3	STK4	Q13043	431
EDIL3	COL4A1	P02462	426
EDIL3	RBPJ	Q06330	425

IntAct

39 interactions, top by confidence:

A	B	Type	Score
NUFIP1	PDE2A	psi-mi:“MI:0914”(association)	0.530
Pafah1b1	EDIL3	psi-mi:“MI:0915”(physical association)	0.400
	AGPS	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
Pik3r2	EDIL3	psi-mi:“MI:0914”(association)	0.350
RYBP	PIPSL	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
CCL3	KRBA1	psi-mi:“MI:0914”(association)	0.350
GPM6A	KIF2A	psi-mi:“MI:0914”(association)	0.350
HAX1	DNM1L	psi-mi:“MI:0914”(association)	0.350
MATN3	EDIL3	psi-mi:“MI:0914”(association)	0.350
SLC38A6	EDIL3	psi-mi:“MI:0914”(association)	0.350
EDIL3	ADGRL1	psi-mi:“MI:0914”(association)	0.350
CACYBP	VPS37C	psi-mi:“MI:0914”(association)	0.350
CACYBP	PSMD11	psi-mi:“MI:0914”(association)	0.350
CAPRIN1	VPS37C	psi-mi:“MI:0914”(association)	0.350
CAPRIN1	SDCBP	psi-mi:“MI:0914”(association)	0.350
CFL2	VPS37C	psi-mi:“MI:0914”(association)	0.350
CSDE1	VPS37C	psi-mi:“MI:0914”(association)	0.350
EIF4A1	SNAP23	psi-mi:“MI:0914”(association)	0.350
FNTA	SDCBP	psi-mi:“MI:0914”(association)	0.350
TSC22D3	VPS37C	psi-mi:“MI:0914”(association)	0.350
CD226	TMED7-TICAM2	psi-mi:“MI:0914”(association)	0.350
EDIL3	ITGAV	psi-mi:“MI:0914”(association)	0.350
CDKL1	EDIL3	psi-mi:“MI:0914”(association)	0.350

BioGRID (53): EDIL3 (Affinity Capture-MS), EDIL3 (Affinity Capture-MS), EDIL3 (Affinity Capture-MS), EDIL3 (Affinity Capture-MS), TF (Affinity Capture-MS), ITGB5 (Affinity Capture-MS), LPHN1 (Affinity Capture-MS), EDIL3 (Affinity Capture-MS), ITGB5 (Affinity Capture-MS), EDIL3 (Affinity Capture-MS), ZNF496 (Affinity Capture-MS), TF (Affinity Capture-MS), LPHN1 (Affinity Capture-MS), ITGAV (Affinity Capture-MS), HADHB (Co-fractionation)

ESM2 similar proteins: O15537, O35276, O35375, O35474, O42163, O42596, O43405, O43854, O60242, O60462, O75077, O75882, O95970, P15209, P21956, P24786, P26012, P51641, P70490, P79385, P84552, Q03351, Q16288, Q16620, Q1EGL2, Q5EA64, Q5IS37, Q5IS82, Q5R7K9, Q5R945, Q5VV63, Q62507, Q63604, Q63769, Q6A051, Q6IS24, Q7TT15, Q80ZF8, Q91044, Q91987

Diamond homologs: A0A1F4, D3ZHH1, G5EDK5, O35474, O43854, O88277, P10040, P13508, P14585, P18168, P78504, P97607, Q06561, Q19319, Q20911, Q501P1, Q53RD9, Q5R7K9, Q5ZQU0, Q63722, Q6R8J2, Q70E20, Q8TER0, Q90Y54, Q90Y57, Q9JLB4, Q9QXX0, Q9QYE5, Q9W332, Q9Y219, A2RUV9, A5A6K7, O14786, O17754, O18806, O35276, O35375, O54858, O54991, O60462

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3479 predictions. Top by Δscore:

Variant	Effect	Δscore
5:83963200:CTTA:C	donor_loss	1.0000
5:83963201:TTAC:T	donor_loss	1.0000
5:83963202:TACCT:T	donor_loss	1.0000
5:83963203:A:AC	donor_gain	1.0000
5:83963204:C:CC	donor_gain	1.0000
5:83963358:CACCT:C	acceptor_gain	1.0000
5:83963360:CCT:C	acceptor_gain	1.0000
5:83963362:T:C	acceptor_gain	1.0000
5:84060294:CTTTA:C	donor_loss	1.0000
5:84060295:TTTAC:T	donor_loss	1.0000
5:84060296:TTAC:T	donor_loss	1.0000
5:84060297:TAC:T	donor_loss	1.0000
5:84060298:AC:A	donor_loss	1.0000
5:84060299:C:CA	donor_loss	1.0000
5:84060299:CCTG:C	donor_gain	1.0000
5:84060301:TGTA:T	donor_gain	1.0000
5:84060480:ACAAC:A	acceptor_gain	1.0000
5:84060481:CAAC:C	acceptor_gain	1.0000
5:84060481:CAACC:C	acceptor_gain	1.0000
5:84060482:AAC:A	acceptor_gain	1.0000
5:84060483:AC:A	acceptor_gain	1.0000
5:84060483:ACCTG:A	acceptor_loss	1.0000
5:84060484:CC:C	acceptor_gain	1.0000
5:84060484:CCTGA:C	acceptor_loss	1.0000
5:84060485:C:CC	acceptor_gain	1.0000
5:84060485:CTGAA:C	acceptor_loss	1.0000
5:84060486:T:G	acceptor_loss	1.0000
5:84064693:GACTT:G	donor_loss	1.0000
5:84064694:ACTT:A	donor_loss	1.0000
5:84064695:CTT:C	donor_loss	1.0000

AlphaMissense

3160 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:83943453:C:G	R470P	1.000
5:84060338:A:G	W367R	1.000
5:84060338:A:T	W367R	1.000
5:84106687:A:G	W205R	1.000
5:84106687:A:T	W205R	1.000
5:83943554:A:C	N436K	0.999
5:83943554:A:T	N436K	0.999
5:83963286:A:C	F404L	0.999
5:83963286:A:T	F404L	0.999
5:83963288:A:G	F404L	0.999
5:83963314:C:T	G395E	0.999
5:83963315:C:G	G395R	0.999
5:83963315:C:T	G395R	0.999
5:83963317:T:G	Q394P	0.999
5:84060336:C:A	W367C	0.999
5:84060336:C:G	W367C	0.999
5:84064729:C:G	R308P	0.999
5:84106685:C:A	W205C	0.999
5:84106685:C:G	W205C	0.999
5:84137248:A:C	C154W	0.999
5:84137309:C:G	C134S	0.999
5:84137310:A:G	C134R	0.999
5:84137310:A:T	C134S	0.999
5:84180400:A:C	C116W	0.999
5:84180401:C:A	C116F	0.999
5:84180401:C:G	C116S	0.999
5:84180401:C:T	C116Y	0.999
5:84180402:A:G	C116R	0.999
5:84180402:A:T	C116S	0.999
5:84180482:C:G	C89S	0.999

dbSNP variants (sampled 300 via entrez): RS1000002658 (5:84060672 T>A,C), RS1000008048 (5:84142375 C>A,T), RS1000013056 (5:84225802 A>G), RS1000015828 (5:84010377 T>G), RS1000017822 (5:84165702 A>G), RS1000018225 (5:83950248 G>A), RS1000020077 (5:84146363 T>C), RS1000020982 (5:84012693 T>G), RS1000023821 (5:84186236 A>G,T), RS1000026512 (5:84187504 A>T), RS1000030891 (5:84297639 G>A), RS1000048704 (5:84131775 C>T), RS1000054906 (5:84324226 C>A), RS1000071176 (5:84010569 T>A,C), RS1000072024 (5:83966920 C>T)

Disease associations

OMIM: gene MIM:606018 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST000628_3	Chemerin levels	1.000000e-06
GCST001345_1	Ankylosing spondylitis	9.000000e-10
GCST001868_11	Alzheimer’s disease biomarkers	8.000000e-07
GCST002041_5	Blood trace element (Cu levels)	2.000000e-06
GCST002322_16	Asthma and hay fever	5.000000e-07
GCST002616_13	Mitochondrial DNA levels	9.000000e-06
GCST003264_127	Post bronchodilator FEV1/FVC ratio	2.000000e-06
GCST003771_11	Loneliness	6.000000e-06
GCST003992_6	Photic sneeze reflex	1.000000e-10
GCST006618_3	Uterine fibroid size (maximum dimension)	8.000000e-07
GCST008559_7	Anxiety and stress-related disorders	1.000000e-06

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004573	chemerin measurement
EFO:0005194	amyloid-beta measurement
EFO:0005267	serum copper measurement
EFO:0006312	mitochondrial DNA measurement
EFO:0004713	FEV/FVC ratio
EFO:0007865	loneliness measurement
EFO:0007887	autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0009410	uterine fibroid measurement
EFO:0010098	stress-related disorder

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1862167	EDIL3		0.00	0

CTD chemical–gene interactions

50 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, increases expression	5
Benzo(a)pyrene	affects methylation, increases expression	4
Aflatoxin B1	decreases expression, decreases methylation, increases methylation	3
Nickel	decreases expression	2
Phenylmercuric Acetate	increases expression, affects cotreatment	2
Tretinoin	increases expression	2
aristolochic acid I	decreases expression	1
geldanamycin	increases expression	1
methyleugenol	decreases expression	1
withaferin A	decreases expression	1
cobaltous chloride	decreases expression	1
benzo(e)pyrene	decreases methylation	1
ferrous chloride	increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
nickel sulfate	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
incobotulinumtoxinA	decreases expression	1
Dasatinib	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Copper	affects binding, increases expression	1
Coumestrol	affects cotreatment, decreases expression	1
Curcumin	decreases expression	1
Diethylhexyl Phthalate	increases expression	1
Disulfiram	increases expression, affects binding	1
Doxorubicin	decreases expression	1

Clinical trials (associated diseases)

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