EMILIN3

Summary

EMILIN3 (elastin microfibril interfacer 3, HGNC:16123) is a protein-coding gene on chromosome 20q12, encoding EMILIN-3 (Q9NT22).

Enables identical protein binding activity. Located in collagen-containing extracellular matrix.

Source: NCBI Gene 90187 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 154 total
• MANE Select transcript: NM_052846

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16123
Approved symbol	EMILIN3
Name	elastin microfibril interfacer 3
Location	20q12
Locus type	gene with protein product
Status	Approved
Aliases	dJ620E11.4
Ensembl gene	ENSG00000183798
Ensembl biotype	protein_coding
OMIM	608929
Entrez	90187

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000332312

RefSeq mRNA: 1 — MANE Select: NM_052846 NM_052846

CCDS: CCDS13316

Canonical transcript exons

ENST00000332312 — 4 exons

Exon	Start	End
ENSE00001409453	41363638	41363861
ENSE00001409950	41365035	41365157
ENSE00003988559	41359962	41363054
ENSE00003988570	41366468	41366818

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 97.16.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2276 / max 8.6850, expressed in 144 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
187282	0.8789	378
187284	0.2276	144

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	97.16	gold quality
caput epididymis	UBERON:0004358	95.28	gold quality
cauda epididymis	UBERON:0004360	92.31	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.65	silver quality
tibia	UBERON:0000979	83.66	gold quality
ventricular zone	UBERON:0003053	82.43	gold quality
cartilage tissue	UBERON:0002418	81.62	gold quality
jejunal mucosa	UBERON:0000399	81.01	gold quality
tibial nerve	UBERON:0001323	80.20	gold quality
apex of heart	UBERON:0002098	76.52	gold quality
ganglionic eminence	UBERON:0004023	76.52	gold quality
ileal mucosa	UBERON:0000331	75.98	gold quality
upper leg skin	UBERON:0004262	75.63	gold quality
right ovary	UBERON:0002118	75.57	gold quality
pigmented layer of retina	UBERON:0001782	74.52	gold quality
left ovary	UBERON:0002119	73.75	gold quality
seminal vesicle	UBERON:0000998	72.91	gold quality
ovary	UBERON:0000992	72.71	gold quality
endocervix	UBERON:0000458	72.23	gold quality
endothelial cell	CL:0000115	71.99	silver quality
cardiac muscle of right atrium	UBERON:0003379	71.71	gold quality
sural nerve	UBERON:0015488	71.66	gold quality
left ventricle myocardium	UBERON:0006566	71.46	gold quality
mucosa of paranasal sinus	UBERON:0005030	71.23	gold quality
heart left ventricle	UBERON:0002084	71.05	gold quality
primary visual cortex	UBERON:0002436	70.83	gold quality
cardiac ventricle	UBERON:0002082	70.70	gold quality
prostate gland	UBERON:0002367	70.64	gold quality
tibialis anterior	UBERON:0001385	70.55	silver quality
right atrium auricular region	UBERON:0006631	70.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting EMILIN3, 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-4533	100.00	69.48	2758
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-4708-3P	99.51	67.99	870
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-3140-5P	99.39	69.04	1136
HSA-MIR-520F-5P	99.34	70.40	1632
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-6744-3P	99.22	64.41	972

Literature-anchored findings (GeneRIF, showing 4)

• EMILIN-5 gene plays an important role in skeletal development(EMILIN-5) (PMID:14706625)
• Might play important roles in carcinogenesis of esophageal cancer. (PMID:18158787)
• characterization of the expression and biochemical properties of EMILIN-3 (PMID:22334695)
• This study identified and validated a three-gene (EMP3, GSX2 and EMILIN3) prognostic signature in Lower-Grade Gliomas. (PMID:29794476)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000076299
danio_rerio	emilin3a	ENSDARG00000078052
mus_musculus	Emilin3	ENSMUSG00000050700
rattus_norvegicus	Emilin3	ENSRNOG00000016734

Paralogs (4): EMILIN2 (ENSG00000132205), EMILIN1 (ENSG00000138080), MMRN1 (ENSG00000138722), MMRN2 (ENSG00000173269)

Protein

Protein identifiers

EMILIN-3 — Q9NT22 (reviewed: Q9NT22)

Alternative names: EMILIN-5, Elastin microfibril interface-located protein 3, Elastin microfibril interface-located protein 5

All UniProt accessions (1): Q9NT22

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NT22-1	1	yes
Q9NT22-2	2

RefSeq proteins (1): NP_443078* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011489	EMI_domain	Domain
IPR050392	Collagen/C1q_domain	Family

Pfam: PF07546

UniProt features (17 total): glycosylation site 5, disulfide bond 3, coiled-coil region 3, signal peptide 1, chain 1, splice variant 1, sequence variant 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NT22-F1	69.27	0.26

Functional residue map

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

Disulfide bonds (3): 59–121, 86–92, 120–129

Glycosylation sites (5): 616, 732, 66, 443, 562

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-2129379	Molecules associated with elastic fibres

MSigDB gene sets: 71 (showing top): AP4_Q6, CAGCTG_AP4_Q5, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, POU3F2_02, chr20q12, TGGAAA_NFAT_Q4_01, YATGNWAAT_OCT_C, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3K27ME3, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, MARTENS_TRETINOIN_RESPONSE_UP

GO Biological Process (0):

GO Molecular Function (3): extracellular matrix constituent conferring elasticity (GO:0030023), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (3): cytoplasm (GO:0005737), extracellular matrix (GO:0031012), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Elastic fibre formation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
extracellular matrix structural constituent	1
structural molecule activity conferring elasticity	1
protein binding	1
binding	1
intracellular anatomical structure	1
external encapsulating structure	1

Protein interactions and networks

STRING

64 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EMILIN3	POLR1H	Q9P1U0	646
EMILIN3	EMID1	Q96A84	411
EMILIN3	HBEGF	Q99075	165
EMILIN3	HIF3A	Q9Y2N7	115
EMILIN3	ERLEC1	Q96DZ1	0
EMILIN3	OLFM4	Q6UX06	0
EMILIN3	DDX39A	O00148	0
EMILIN3	CSN1S1	P47710	0
EMILIN3	WDR76	Q9H967	0
EMILIN3	GID8	Q9NWU2	0
EMILIN3	TARBP2	Q15633	0
EMILIN3	LEFTY1	O75610	0
EMILIN3	MMP10	P09238	0
EMILIN3	RMND5A	Q9H871	0
EMILIN3	SCARA3	Q6AZY7	0
EMILIN3	KLRG2	A4D1S0	0
EMILIN3	LEFTY2	O00292	0
EMILIN3	HOXA3	O43365	0
EMILIN3	CCL4	P13236	0
EMILIN3	TAF1	P21675	0
EMILIN3	NUP153	P49790	0
EMILIN3	YPEL5	P62699	0

IntAct

62 interactions, top by confidence:

A	B	Type	Score
KBTBD7	METTL15	psi-mi:“MI:0914”(association)	0.730
GORASP2	EMILIN3	psi-mi:“MI:0915”(physical association)	0.560
EMILIN3	FBXO28	psi-mi:“MI:0915”(physical association)	0.560
EMILIN3	MEMO1	psi-mi:“MI:0915”(physical association)	0.560
SDCBP	EMILIN3	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	EMILIN3	psi-mi:“MI:0915”(physical association)	0.560
NTAQ1	EMILIN3	psi-mi:“MI:0915”(physical association)	0.560
BCAS2	EMILIN3	psi-mi:“MI:0915”(physical association)	0.560
EMILIN3	EMILIN3	psi-mi:“MI:0915”(physical association)	0.560
KLRG2	GXYLT2	psi-mi:“MI:0914”(association)	0.530
VWCE	ZNF316	psi-mi:“MI:0914”(association)	0.530
MMP10	TIMP1	psi-mi:“MI:0914”(association)	0.530
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
EMILIN3	ZZEF1	psi-mi:“MI:0914”(association)	0.530
PLAUR	DDX11L8	psi-mi:“MI:0914”(association)	0.350
TRIM10	POLRMT	psi-mi:“MI:0914”(association)	0.350
CSN1S1	HSPA5	psi-mi:“MI:0914”(association)	0.350
	MYO9A	psi-mi:“MI:0914”(association)	0.350
SQSTM1	CHEK1	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
LURAP1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
FBLN5	ZNF320	psi-mi:“MI:0914”(association)	0.350
PNMA2	TARS3	psi-mi:“MI:0914”(association)	0.350
ARMC8	VWA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (65): EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Affinity Capture-MS), EMILIN3 (Two-hybrid), EMILIN3 (Two-hybrid), EMILIN3 (Two-hybrid)

ESM2 similar proteins: A2AV25, A5PJQ2, A5PMY6, A6H6E2, B7ZNG0, O00548, O35764, O43278, O70340, O95502, P21757, P21758, P30204, P47970, P47971, P47972, P48759, P58660, P59900, P97738, Q05585, Q15818, Q24K15, Q2M1P5, Q5RFW0, Q61483, Q62443, Q6AZY7, Q6MG84, Q6ZMJ2, Q86VZ4, Q8BJS4, Q8C850, Q8CB67, Q8K299, Q8N539, Q8NI99, Q8R0Z6, Q95LU3, Q96NZ8

Diamond homologs: A6H6E2, F1QC17, P59900, Q13201, Q8K482, Q91VF6, Q96A83, Q96A84, Q99K41, Q9BXX0, Q9H8L6, Q9NT22, Q9Y6C2, Q91VF5, B2RPV6, Q05A80, Q5RJ80, Q6IMN6, Q8R066, Q9BXJ3, Q9W332, Q4ZJM7, Q5FVH0, Q8K479, Q9BXJ0, A6NHN0, Q0II24

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	141
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

663 predictions. Top by Δscore:

Variant	Effect	Δscore
20:41366466:A:AC	donor_gain	1.0000
20:41366467:C:CC	donor_gain	1.0000
20:41365033:A:AC	donor_gain	0.9900
20:41365034:C:CC	donor_gain	0.9900
20:41365034:CGTGA:C	donor_gain	0.9900
20:41366462:GCTTA:G	donor_loss	0.9900
20:41366463:CTTA:C	donor_loss	0.9900
20:41366464:TTAC:T	donor_loss	0.9900
20:41366465:TACT:T	donor_loss	0.9900
20:41366466:ACTTG:A	donor_loss	0.9900
20:41366467:C:CA	donor_loss	0.9900
20:41366467:CT:C	donor_gain	0.9900
20:41366467:CTT:C	donor_gain	0.9900
20:41365027:GCACT:G	donor_loss	0.9800
20:41365028:CACT:C	donor_loss	0.9800
20:41365029:ACTT:A	donor_loss	0.9800
20:41365030:CT:C	donor_loss	0.9800
20:41365031:TTA:T	donor_loss	0.9800
20:41365032:T:TC	donor_loss	0.9800
20:41365156:CC:C	acceptor_gain	0.9800
20:41365157:CC:C	acceptor_gain	0.9800
20:41365026:TGCAC:T	donor_loss	0.9700
20:41366467:CTTG:C	donor_gain	0.9600
20:41366467:CTTGT:C	donor_gain	0.9600
20:41363051:CTTC:C	acceptor_gain	0.9500
20:41365156:CCCTA:C	acceptor_loss	0.9500
20:41365157:CCT:C	acceptor_loss	0.9500
20:41365159:T:A	acceptor_loss	0.9500
20:41363868:C:CT	acceptor_gain	0.9400
20:41365034:CG:C	donor_gain	0.9300

AlphaMissense

4866 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:41363798:C:A	W118C	0.977
20:41363798:C:G	W118C	0.977
20:41361818:A:G	I584T	0.974
20:41361809:A:G	L587P	0.973
20:41361797:A:G	L591P	0.969
20:41361776:A:G	L598P	0.963
20:41361818:A:C	I584S	0.955
20:41361809:A:T	L587H	0.950
20:41363836:A:C	Y106D	0.946
20:41361755:A:T	V605D	0.940
20:41361780:A:G	S597P	0.940
20:41361767:A:G	L601P	0.936
20:41363835:T:G	Y106S	0.936
20:41361792:A:G	S593P	0.935
20:41365149:C:G	C59S	0.935
20:41365150:A:T	C59S	0.935
20:41361812:A:G	L586P	0.928
20:41361887:A:G	L561P	0.926
20:41361805:C:A	K588N	0.922
20:41361805:C:G	K588N	0.922
20:41363835:T:C	Y106C	0.911
20:41365122:G:A	T68I	0.911
20:41361809:A:C	L587R	0.909
20:41363800:A:G	W118R	0.907
20:41363800:A:T	W118R	0.907
20:41361759:A:G	S604P	0.897
20:41361776:A:T	L598H	0.895
20:41365085:C:A	K80N	0.895
20:41365085:C:G	K80N	0.895
20:41365061:C:A	W88C	0.894

dbSNP variants (sampled 300 via entrez): RS1000120241 (20:41366670 GC>G,GCC), RS1000216539 (20:41360358 T>C), RS1000407103 (20:41366459 C>A,G,T), RS1000645943 (20:41366024 G>A,T), RS1000923589 (20:41359837 TC>T), RS1001494274 (20:41364305 C>T), RS1001544376 (20:41365277 T>C), RS1001659216 (20:41365536 C>T), RS1001669688 (20:41359635 G>C), RS1001803721 (20:41360763 A>T), RS1002550574 (20:41363870 G>A), RS1002807087 (20:41359542 G>A,C), RS1005154508 (20:41360263 G>A,C), RS1005527465 (20:41364119 G>A), RS1005642086 (20:41364411 C>CAGGGA)

Disease associations

OMIM: gene MIM:608929 | 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

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Panobinostat	affects cotreatment, decreases expression	2
Benzo(a)pyrene	increases expression, affects methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	affects expression, increases methylation	2
ethyl-p-hydroxybenzoate	decreases expression	1
trichostatin A	decreases expression	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Vorinostat	affects cotreatment, decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Nickel	decreases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Cyclosporine	decreases expression	1
Sodium Selenite	decreases expression	1

Clinical trials (associated diseases)

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