EBLN1

Summary

EBLN1 (endogenous Bornavirus like nucleoprotein 1, HGNC:39430) is a protein-coding gene on chromosome 10p12.31, encoding Endogenous Bornavirus-like nucleoprotein 1 (P0CF75). May act as an RNA-binding protein.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 56 total
• MANE Select transcript: NM_001394757

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:39430
Approved symbol	EBLN1
Name	endogenous Bornavirus like nucleoprotein 1
Location	10p12.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000223601
Ensembl biotype	protein_coding
OMIM	613249
Entrez	340900

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000422359, ENST00000939589

RefSeq mRNA: 2 — MANE Select: NM_001394757 NM_001199938, NM_001394757

CCDS: CCDS60498

Canonical transcript exons

ENST00000422359 — 3 exons

Exon	Start	End
ENSE00001764833	22208475	22210027
ENSE00003924445	22217916	22218015
ENSE00003935864	22212842	22212965

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 96.65.

Top tissues by expression

101 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	96.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.81	gold quality
right testis	UBERON:0004534	59.02	gold quality
testis	UBERON:0000473	58.33	gold quality
left testis	UBERON:0004533	58.30	gold quality
granulocyte	CL:0000094	39.85	gold quality
bone marrow cell	CL:0002092	38.50	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
mucosa of stomach	UBERON:0001199	35.85	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
bone marrow	UBERON:0002371	34.19	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
ectocervix	UBERON:0012249	31.99	gold quality
uterine cervix	UBERON:0000002	31.74	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	30.90	silver quality
fallopian tube	UBERON:0003889	30.42	gold quality
right uterine tube	UBERON:0001302	30.25	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
substantia nigra	UBERON:0002038	29.75	silver quality
left uterine tube	UBERON:0001303	29.57	gold quality
Brodmann (1909) area 9	UBERON:0013540	29.04	gold quality
leukocyte	CL:0000738	28.90	gold quality
myometrium	UBERON:0001296	28.71	gold quality
liver	UBERON:0002107	28.32	gold quality
monocyte	CL:0000576	28.29	gold quality
duodenum	UBERON:0002114	28.14	gold quality
islet of Langerhans	UBERON:0000006	28.09	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.80

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

• Our results provide evidence for new loci influencing abdominal visceral (BBS9, ADCY8, KCNK9) and subcutaneous (MLLT10/DNAJC1/EBLN1) fat, and confirmed a locus (THNSL2) previously reported to be associated with abdominal fat in women. (PMID:26480920)
• Numerous genes were dysregulated by Endogenous bornavirus-like nucleoprotein 1 silencing, some of which may be key target genes of Rho family GTPase 3, oncostatin M receptor, and cAMP responsive element binding protein 3-like 2 protein. (PMID:27023521)
• human EBLN1 possesses important cellular functions within human cells. (PMID:27739501)

Cross-species orthologs

0 orthologs

Paralogs (1): EBLN2 (ENSG00000255423)

Protein

Protein identifiers

Endogenous Bornavirus-like nucleoprotein 1 — P0CF75 (reviewed: P0CF75)

Alternative names: Endogenous Borna-like N element-1

All UniProt accessions (1): P0CF75

UniProt curated annotations — full annotation on UniProt →

Function. May act as an RNA-binding protein. Highly homologous to the bornavirus nucleocapsid N protein that binds viral RNA and oligomerizes.

Tissue specificity. Expression detected by RT-PCR in a few cell lines, including OL, HEK293T and MOLT-4. Not observed in HeLa cells.

Miscellaneous. Bornavirus is a non-retroviral RNA virus that does not generate DNA forms during viral replication. Therefore, integration of EBLN-1 must have occur through a mechanism relying on an endogenous reverse transcriptase activity.

RefSeq proteins (2): NP_001186867, NP_001381686* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009441	P40_nucleoprot_BD-vir	Family
IPR015969	P40_nucleoprot_sub1_BD-vir	Homologous_superfamily
IPR015970	P40_nucleoprot_sub2_BD-vir	Homologous_superfamily
IPR036260	P40_nucleoprot_sf_BD-vir	Homologous_superfamily

Pfam: PF06407

UniProt features (5 total): sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CF75-F1	84.45	0.61

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 3 (showing top): chr10p12, PAX3_TARGET_GENES, SUPT16H_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

150 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EBLN1	LIME1	Q9H400	518
EBLN1	C16orf96	A6NNT2	505
EBLN1	AP1S1	P61966	493
EBLN1	FAM194C	Q8ND61	479
EBLN1	ZNF284	Q2VY69	476
EBLN1	FANCC	Q00597	413
EBLN1	YAE1	Q9NRH1	400
EBLN1	LRRC46	Q96FV0	377
EBLN1	MYCBPAP	Q8TBZ2	370
EBLN1	KRTAP2-3	P0C7H8	353
EBLN1	V9GYV3	V9GYV3	353
EBLN1	ETNK1	Q9HBU6	348
EBLN1	GPR45	Q9Y5Y3	325
EBLN1	TLL2	Q9Y6L7	311
EBLN1	WDR46	O15213	308

IntAct

3 interactions, top by confidence:

A	B	Type	Score
EBLN1	TTN	psi-mi:“MI:0915”(physical association)	0.400
EBLN1	STAG2	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (3): EBLN1 (Affinity Capture-MS), STAG2 (Proximity Label-MS), TTN (Proximity Label-MS)

ESM2 similar proteins: A0A345BJN9, A1XFV8, A3DRP6, A3RM21, A7WNB1, A8C8K0, B2ZCQ0, F5HDY6, P03499, P04858, P07051, P08593, P08671, P09280, P0C772, P0C773, P0CF75, P0DOE1, P13140, P14155, P21431, P22046, P31964, P47146, P52510, Q00151, Q04551, Q07458, Q07FH9, Q0GBY2, Q197F9, Q1I0U5, Q289M1, Q5K2K5, Q5NDN1, Q65YU7, Q6P5S2, Q6XSW4, Q6XTD8, Q6XTK0

Diamond homologs: P0C796, P0C797, P0CF75, Q6P2I7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

193 predictions. Top by Δscore:

Variant	Effect	Δscore
10:22209350:C:CT	acceptor_gain	0.6800
10:22209484:G:A	donor_gain	0.6100
10:22209447:TTC:T	donor_gain	0.5600
10:22209080:C:CC	acceptor_gain	0.5500
10:22209161:GTACC:G	donor_loss	0.5100
10:22209162:TACC:T	donor_loss	0.5100
10:22209163:A:AC	donor_gain	0.5100
10:22209163:ACCTT:A	donor_loss	0.5100
10:22209164:C:CC	donor_gain	0.5100
10:22209164:C:CG	donor_loss	0.5100
10:22209349:C:G	acceptor_gain	0.5100
10:22209032:C:CT	acceptor_gain	0.4900
10:22208973:C:CT	acceptor_gain	0.4800
10:22209261:T:A	donor_gain	0.4800
10:22208976:T:C	acceptor_gain	0.4600
10:22209351:A:T	acceptor_gain	0.4600
10:22209079:GCT:G	acceptor_gain	0.4500
10:22209163:AC:A	donor_gain	0.4500
10:22209164:CC:C	donor_gain	0.4500
10:22209350:C:T	acceptor_gain	0.4500
10:22209448:T:A	donor_gain	0.4500
10:22209465:T:TA	donor_gain	0.4500
10:22209206:C:G	acceptor_gain	0.4400
10:22209077:TTG:T	acceptor_gain	0.4300
10:22208981:G:GC	acceptor_gain	0.4200
10:22209080:C:A	acceptor_gain	0.4200
10:22209205:T:TG	acceptor_gain	0.4100
10:22209033:A:T	acceptor_gain	0.4000
10:22209076:GTTGC:G	acceptor_gain	0.4000
10:22209077:TTGCT:T	acceptor_gain	0.4000

AlphaMissense

2420 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:22209090:G:C	F298L	0.932
10:22209090:G:T	F298L	0.932
10:22209092:A:G	F298L	0.932
10:22209741:A:C	F81L	0.922
10:22209741:A:T	F81L	0.922
10:22209743:A:G	F81L	0.922
10:22209255:G:C	F243L	0.902
10:22209255:G:T	F243L	0.902
10:22209257:A:G	F243L	0.902
10:22209768:A:C	F72L	0.897
10:22209768:A:T	F72L	0.897
10:22209770:A:G	F72L	0.897
10:22209192:A:C	F264L	0.874
10:22209192:A:T	F264L	0.874
10:22209194:A:G	F264L	0.874
10:22209489:G:C	F165L	0.873
10:22209489:G:T	F165L	0.873
10:22209491:A:G	F165L	0.873
10:22209027:A:C	F319L	0.869
10:22209027:A:T	F319L	0.869
10:22209029:A:G	F319L	0.869
10:22209894:A:C	F30L	0.864
10:22209894:A:T	F30L	0.864
10:22209896:A:G	F30L	0.864
10:22209342:A:C	F214L	0.856
10:22209342:A:T	F214L	0.856
10:22209344:A:G	F214L	0.856
10:22209036:A:C	F316L	0.854
10:22209036:A:T	F316L	0.854
10:22209038:A:G	F316L	0.854

dbSNP variants (sampled 300 via entrez): RS1000350251 (10:22210331 A>G), RS1000834713 (10:22215093 T>C), RS1001448761 (10:22210680 T>C), RS1001853304 (10:22208911 C>A,G,T), RS1001870101 (10:22215168 A>G), RS1001919703 (10:22210355 T>C), RS1001962018 (10:22217931 G>A), RS1002566736 (10:22208424 G>C), RS1002671631 (10:22217764 A>C), RS1003046846 (10:22211464 A>T), RS1003195834 (10:22208090 G>A,T), RS1003212263 (10:22219281 C>T), RS1003226317 (10:22212867 T>C), RS1003737828 (10:22219698 G>A), RS1003902965 (10:22215686 G>A,T)

Disease associations

OMIM: gene MIM:613249 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST003170_7	Subcutaneous adipose tissue	4.000000e-08
GCST007327_95	Smoking status (ever vs never smokers)	1.000000e-09
GCST007507_12	Benign prostatic hyperplasia and lower urinary tract symptoms	2.000000e-15
GCST010136_13	Fruit consumption	1.000000e-08
GCST010136_20	Fruit consumption	3.000000e-08
GCST010136_26	Fruit consumption	5.000000e-20
GCST010142_85	Fish- and plant-related diet	2.000000e-24
GCST011351_16	Aspartate aminotransferase levels	2.000000e-09

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004318	smoking behavior
EFO:0008008	lower urinary tract symptom
EFO:0008111	diet measurement
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
abrine	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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