EBLN2

Summary

EBLN2 (endogenous Bornavirus like nucleoprotein 2, HGNC:25493) is a protein-coding gene on chromosome 3p13, encoding Endogenous Bornavirus-like nucleoprotein 2 (Q6P2I7). May act as an RNA-binding protein.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_018029

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25493
Approved symbol	EBLN2
Name	endogenous Bornavirus like nucleoprotein 2
Location	3p13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000255423
Ensembl biotype	protein_coding
OMIM	613250
Entrez	55096

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000533473

RefSeq mRNA: 1 — MANE Select: NM_018029 NM_018029

CCDS: CCDS54608

Canonical transcript exons

ENST00000533473 — 1 exons

Exon	Start	End
ENSE00002183812	73061659	73063337

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 84.74.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	84.74	gold quality
endothelial cell	CL:0000115	83.54	gold quality
nipple	UBERON:0002030	82.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.46	gold quality
tibia	UBERON:0000979	80.41	gold quality
cervix squamous epithelium	UBERON:0006922	80.27	silver quality
mucosa of paranasal sinus	UBERON:0005030	80.06	gold quality
visceral pleura	UBERON:0002401	79.71	gold quality
trabecular bone tissue	UBERON:0002483	79.48	gold quality
thymus	UBERON:0002370	78.67	gold quality
oviduct epithelium	UBERON:0004804	78.60	gold quality
tendon of biceps brachii	UBERON:0008188	78.04	gold quality
inferior olivary complex	UBERON:0002127	77.95	gold quality
bone marrow	UBERON:0002371	77.84	gold quality
pylorus	UBERON:0001166	77.44	gold quality
trachea	UBERON:0003126	77.22	gold quality
bronchus	UBERON:0002185	76.69	gold quality
epithelium of bronchus	UBERON:0002031	76.65	gold quality
parietal pleura	UBERON:0002400	76.32	gold quality
pleura	UBERON:0000977	76.31	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	76.05	gold quality
corpus callosum	UBERON:0002336	75.97	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.82	gold quality
cervix epithelium	UBERON:0004801	75.56	silver quality
sperm	CL:0000019	75.49	silver quality
cartilage tissue	UBERON:0002418	75.43	gold quality
trigeminal ganglion	UBERON:0001675	75.10	gold quality
cardia of stomach	UBERON:0001162	74.95	gold quality
bronchial epithelial cell	CL:0002328	74.89	gold quality
choroid plexus epithelium	UBERON:0003911	74.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting EBLN2, 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-5692A	100.00	74.40	6850
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-4639-5P	99.81	67.37	1028
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-605-5P	98.79	68.24	1161
HSA-MIR-5008-3P	98.73	67.50	1433
HSA-MIR-5581-3P	98.55	70.31	1161
HSA-MIR-4733-5P	97.75	67.44	866
HSA-MIR-4433B-3P	97.22	63.62	663
HSA-MIR-7161-3P	96.79	68.79	798
HSA-MIR-410-5P	96.55	66.28	459
HSA-MIR-549A-5P	96.35	68.08	587
HSA-MIR-323B-5P	96.12	66.39	472
HSA-MIR-1258	96.08	67.74	700
HSA-MIR-494-5P	95.31	66.29	463

Literature-anchored findings (GeneRIF, showing 1)

• A Human Endogenous Bornavirus-Like Nucleoprotein Encodes a Mitochondrial Protein Associated with Cell Viability. (PMID:33952640)

Cross-species orthologs

0 orthologs

Paralogs (1): EBLN1 (ENSG00000223601)

Protein

Protein identifiers

Endogenous Bornavirus-like nucleoprotein 2 — Q6P2I7 (reviewed: Q6P2I7)

Alternative names: Endogenous Borna-like N element-2

All UniProt accessions (1): Q6P2I7

UniProt curated annotations — full annotation on UniProt →

Function. May act as an RNA-binding protein. The C-terminal region is highly homologous to the bornavirus nucleocapsid N protein that binds viral RNA and oligomerizes. The viral protein also possesses a nuclear import and a nuclear export signal. These 2 signals seem absent in EBLN-2 supporting an unrelated function in Human.

Miscellaneous. Bornavirus is a non-retroviral RNA virus that does not generate DNA forms during viral replication. Therefore, integration of EBLN-2 must have occur through a mechanism relying on an endogenous reverse transcriptase activity.

RefSeq proteins (1): NP_060499* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009441	P40_nucleoprot_BD-vir	Family
IPR015969	P40_nucleoprot_sub1_BD-vir	Homologous_superfamily
IPR036260	P40_nucleoprot_sf_BD-vir	Homologous_superfamily

Pfam: PF06407

UniProt features (3 total): chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P2I7-F1	67.89	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): chr3p13, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP, MMEF2_Q6, WANG_CISPLATIN_RESPONSE_AND_XPC_UP, BCAT.100_UP.V1_DN, E2F3_UP.V1_DN, MIR4310, MIR4279, MIR552_5P, MIR605_5P, MIR4733_5P, MIR4639_5P, GSE13485_CTRL_VS_DAY21_YF17D_VACCINE_PBMC_UP, GSE13485_DAY3_VS_DAY21_YF17D_VACCINE_PBMC_UP, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_RUXOLITINIB_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

196 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EBLN2	AP1S1	P61966	719
EBLN2	FANCC	Q00597	626
EBLN2	ZNF311	Q5JNZ3	595
EBLN2	TUSC2	O75896	588
EBLN2	SPDYE3	A6NKU9	570
EBLN2	LIME1	Q9H400	543
EBLN2	TAF1B	Q53T94	447
EBLN2	POU5F2	Q8N7G0	432
EBLN2	FOXP2	O15409	421
EBLN2	FAM124B	Q9H5Z6	419
EBLN2	Q8NG57	Q8NG57	419
EBLN2	XCR1	P46094	418
EBLN2	AP4E1	Q9UPM8	414
EBLN2	ASTN1	O14525	406
EBLN2	ZBTB12	Q9Y330	398

IntAct

11 interactions, top by confidence:

A	B	Type	Score
EBLN2	SCGN	psi-mi:“MI:0914”(association)	0.350
AP1S1	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
TUSC2	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
RAB5IF	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
CAB39	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
PRKAB1	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
WRAP73	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
STK16	EBLN2	psi-mi:“MI:0915”(physical association)	0.000
ATG12	EBLN2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (9): EBLN2 (Synthetic Lethality), EBLN2 (Affinity Capture-MS), EBLN2 (Affinity Capture-MS), EBLN2 (Affinity Capture-MS), EBLN2 (Affinity Capture-MS), EBLN2 (Affinity Capture-MS), EBLN2 (Affinity Capture-MS), GNA13 (Affinity Capture-MS), SCGN (Affinity Capture-MS)

ESM2 similar proteins: A2VDT9, B2ZCQ0, B2ZCQ2, C6Y4A2, F4IVU1, I6LJ77, O70552, O75818, O94245, P04886, P07051, P08593, P08671, P0C6Z9, P13093, P13742, P25223, P29882, P34515, P40101, P40385, P41089, P52465, P83857, Q01045, Q01226, Q0GBX7, Q0GBY2, Q1X711, Q3KSR8, Q567C3, Q5R8K0, Q5UQH7, Q5VKP0, Q64962, Q66672, Q6P2I7, Q6X1D6, Q8B6J7, Q8V3U1

Diamond homologs: P0C796, P0C797, P0CF75, Q6P2I7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

451 predictions. Top by Δscore:

Variant	Effect	Δscore
3:73062376:GATAT:G	donor_gain	1.0000
3:73062305:G:GT	donor_gain	0.9900
3:73062332:GACA:G	donor_gain	0.9900
3:73062385:GACAT:G	donor_gain	0.9800
3:73062456:T:G	donor_gain	0.9700
3:73062336:G:GG	donor_gain	0.9600
3:73063032:TTAAA:T	donor_gain	0.9500
3:73062316:C:G	donor_gain	0.9400
3:73062346:G:GT	donor_gain	0.9400
3:73062222:A:AG	acceptor_gain	0.9300
3:73062305:G:T	donor_gain	0.9200
3:73062401:C:G	donor_gain	0.9100
3:73062324:G:T	donor_gain	0.9000
3:73062335:A:AG	donor_gain	0.9000
3:73062137:G:A	acceptor_gain	0.8100
3:73062883:C:G	donor_gain	0.8000
3:73062306:A:T	donor_gain	0.7900
3:73062827:TTG:T	donor_gain	0.7900
3:73062807:G:GT	donor_gain	0.7800
3:73062235:A:G	acceptor_gain	0.7500
3:73062455:GTTTA:G	donor_gain	0.7500
3:73062613:G:GC	acceptor_gain	0.7500
3:73062148:A:AG	acceptor_gain	0.7400
3:73062149:G:GG	acceptor_gain	0.7400
3:73062281:GGA:G	donor_gain	0.7400
3:73062282:GAG:G	donor_gain	0.7400
3:73062380:T:TG	donor_gain	0.7400
3:73062804:T:TA	donor_gain	0.7300
3:73062898:T:A	donor_gain	0.7200
3:73062722:C:T	donor_gain	0.7100

AlphaMissense

1805 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:73062436:T:C	F119L	0.971
3:73062438:C:A	F119L	0.971
3:73062438:C:G	F119L	0.971
3:73062463:T:C	F128L	0.965
3:73062465:C:A	F128L	0.965
3:73062465:C:G	F128L	0.965
3:73062454:A:C	S125R	0.958
3:73062456:T:A	S125R	0.958
3:73062456:T:G	S125R	0.958
3:73062715:T:C	F212L	0.935
3:73062717:C:A	F212L	0.935
3:73062717:C:G	F212L	0.935
3:73062469:T:C	C130R	0.933
3:73062601:T:C	F174L	0.927
3:73062603:T:A	F174L	0.927
3:73062603:T:G	F174L	0.927
3:73062310:T:C	F77L	0.920
3:73062312:T:A	F77L	0.920
3:73062312:T:G	F77L	0.920
3:73062367:A:C	S96R	0.912
3:73062369:C:A	S96R	0.912
3:73062369:C:G	S96R	0.912
3:73062615:G:C	E178D	0.906
3:73062615:G:T	E178D	0.906
3:73062853:T:C	F258L	0.905
3:73062855:T:A	F258L	0.905
3:73062855:T:G	F258L	0.905
3:73062614:A:T	E178V	0.899
3:73062441:C:A	H120Q	0.898
3:73062441:C:G	H120Q	0.898

dbSNP variants (sampled 300 via entrez): RS1000279281 (3:73062983 G>A,C), RS1000997069 (3:73063252 T>A,G), RS1001478432 (3:73063579 G>A), RS1001666226 (3:73060601 T>C), RS1002123984 (3:73060391 T>C), RS1003082672 (3:73061817 C>G,T), RS1004669542 (3:73060880 T>C), RS1005021018 (3:73061148 AATTT>A), RS1005458027 (3:73060138 A>T), RS1006051239 (3:73061355 G>A,T), RS1006413072 (3:73061601 C>T), RS1006676787 (3:73063439 C>G,T), RS1008013054 (3:73063260 G>A,T), RS1008852190 (3:73060056 A>T), RS1009422798 (3:73059798 G>A)

Disease associations

OMIM: gene MIM:613250 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010002_431	Refractive error	3.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects cotreatment, decreases expression	2
Cadmium Chloride	increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
chloroacetaldehyde	decreases expression	1
ferrous chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
3-hydroxy-4-prenyl-5-methoxystilbene-2-carboxylic acid	increases expression	1
Sunitinib	decreases expression	1
Cidofovir	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Cadmium	increases abundance, increases expression	1
Cisplatin	decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Clodronic Acid	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Oxygen	increases expression	1
Ozone	affects expression, increases abundance	1
Thiram	decreases expression	1
Valproic Acid	affects expression	1
Vincristine	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases expression	1
Lactic Acid	increases expression	1
Vitamin K 3	affects expression	1

Clinical trials (associated diseases)

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