Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	1947
Gene name	Ephrin B1
Gene symbol	EFNB1
Synonyms (NCBI Gene)	CFNDCFNSEFB1EFL3EPLG2Elk-LLERK2
Chromosome	X
Chromosome location	Xq13.1
Summary	The protein encoded by this gene is a type I membrane protein and a ligand of Eph-related receptor tyrosine kinases. It may play a role in cell adhesion and function in the development or maintenance of the nervous system. [provided by RefSeq, Jul 2008]

Show/Hide all (27)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28935170	G>T	Pathogenic	Coding sequence variant, missense variant
rs28936069	G>A	Pathogenic	Coding sequence variant, missense variant
rs28936070	G>T	Pathogenic	Coding sequence variant, missense variant
rs28936071	A>C,G	Pathogenic	Coding sequence variant, missense variant
rs104894796	C>T	Pathogenic	Coding sequence variant, missense variant
rs104894801	C>A,G,T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs104894802	T>G	Pathogenic	Coding sequence variant, missense variant
rs104894803	G>A	Pathogenic	Coding sequence variant, stop gained
rs104894804	C>T	Pathogenic	Coding sequence variant, stop gained
rs587777109	C>T	Pathogenic	Stop gained, coding sequence variant
rs879255545	->CCGTATCCTGGAGC	Pathogenic	Frameshift variant, coding sequence variant
rs886041800	T>G	Pathogenic	Stop gained, coding sequence variant
rs886041811	->G	Pathogenic	Frameshift variant, coding sequence variant
rs1057519033	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1057519034	C>G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs1057519035	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1064793438	AGCTGCCTG>-	Pathogenic	Coding sequence variant, inframe deletion
rs1556096780	T>A	Pathogenic	Splice donor variant
rs1556105849	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1556105875	A>T	Pathogenic	Stop gained, coding sequence variant
rs1556106318	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1556107481	G>A	Likely-pathogenic	Splice donor variant
rs1556107856	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1556107925	AC>-	Pathogenic	Frameshift variant, coding sequence variant
rs1569398276	C>T	Pathogenic	Coding sequence variant, stop gained
rs1602670769	->A	Pathogenic	Coding sequence variant, frameshift variant
rs1602671282	TGAGTG>-	Likely-pathogenic	Splice donor variant, intron variant

157

Show/Hide all (157)

miRTarBase ID	miRNA	Experiments	Reference
MIRT000478	hsa-miR-124-3p	qRT-PCRLuciferase reporter assayWestern blot	20308325
MIRT025289	hsa-miR-34a-5p	Proteomics	21566225
MIRT025289	hsa-miR-34a-5p	Proteomics	21566225
MIRT025289	hsa-miR-34a-5p	Proteomics	21566225
MIRT025289	hsa-miR-34a-5p	Proteomics	21566225
MIRT048918	hsa-miR-92a-3p	CLASH	23622248
MIRT040525	hsa-miR-92b-3p	CLASH	23622248
MIRT462756	hsa-miR-4695-5p	PAR-CLIP	23592263
MIRT462757	hsa-miR-2682-5p	PAR-CLIP	23592263
MIRT462755	hsa-miR-34b-5p	PAR-CLIP	23592263
MIRT462754	hsa-miR-449c-5p	PAR-CLIP	23592263
MIRT462752	hsa-miR-6895-5p	PAR-CLIP	23592263
MIRT462753	hsa-miR-4302	PAR-CLIP	23592263
MIRT462751	hsa-miR-1827	PAR-CLIP	23592263
MIRT462750	hsa-miR-3616-3p	PAR-CLIP	23592263
MIRT462749	hsa-miR-4721	PAR-CLIP	23592263
MIRT462748	hsa-miR-6134	PAR-CLIP	23592263
MIRT462747	hsa-miR-6499-3p	PAR-CLIP	23592263
MIRT462746	hsa-miR-3612	PAR-CLIP	23592263
MIRT462745	hsa-miR-650	PAR-CLIP	23592263
MIRT462744	hsa-miR-3689d	PAR-CLIP	23592263
MIRT462743	hsa-miR-6851-5p	PAR-CLIP	23592263
MIRT462742	hsa-miR-1193	PAR-CLIP	23592263
MIRT025289	hsa-miR-34a-5p	PAR-CLIP	23592263
MIRT462741	hsa-miR-34c-5p	PAR-CLIP	23592263
MIRT462740	hsa-miR-449a	PAR-CLIP	23592263
MIRT462739	hsa-miR-449b-5p	PAR-CLIP	23592263
MIRT462738	hsa-miR-4640-5p	PAR-CLIP	23592263
MIRT462737	hsa-miR-4726-5p	PAR-CLIP	23592263
MIRT462736	hsa-miR-3165	PAR-CLIP	23592263
MIRT462734	hsa-miR-3650	PAR-CLIP	23592263
MIRT462735	hsa-miR-4316	PAR-CLIP	23592263
MIRT462733	hsa-miR-1294	PAR-CLIP	23592263
MIRT462732	hsa-miR-7847-3p	PAR-CLIP	23592263
MIRT462731	hsa-miR-3691-5p	PAR-CLIP	23592263
MIRT462730	hsa-miR-3911	PAR-CLIP	23592263
MIRT462729	hsa-miR-1226-5p	PAR-CLIP	23592263
MIRT462728	hsa-miR-432-3p	PAR-CLIP	23592263
MIRT462727	hsa-miR-30b-3p	PAR-CLIP	23592263
MIRT462730	hsa-miR-3911	HITS-CLIP	27418678
MIRT462756	hsa-miR-4695-5p	PAR-CLIP	23592263
MIRT462757	hsa-miR-2682-5p	PAR-CLIP	23592263
MIRT462755	hsa-miR-34b-5p	PAR-CLIP	23592263
MIRT462754	hsa-miR-449c-5p	PAR-CLIP	23592263
MIRT462752	hsa-miR-6895-5p	PAR-CLIP	23592263
MIRT462753	hsa-miR-4302	PAR-CLIP	23592263
MIRT462751	hsa-miR-1827	PAR-CLIP	23592263
MIRT462750	hsa-miR-3616-3p	PAR-CLIP	23592263
MIRT462749	hsa-miR-4721	PAR-CLIP	23592263
MIRT462748	hsa-miR-6134	PAR-CLIP	23592263
MIRT462747	hsa-miR-6499-3p	PAR-CLIP	23592263
MIRT462746	hsa-miR-3612	PAR-CLIP	23592263
MIRT462745	hsa-miR-650	PAR-CLIP	23592263
MIRT462744	hsa-miR-3689d	PAR-CLIP	23592263
MIRT462743	hsa-miR-6851-5p	PAR-CLIP	23592263
MIRT462742	hsa-miR-1193	PAR-CLIP	23592263
MIRT025289	hsa-miR-34a-5p	PAR-CLIP	23592263
MIRT462741	hsa-miR-34c-5p	PAR-CLIP	23592263
MIRT462740	hsa-miR-449a	PAR-CLIP	23592263
MIRT462739	hsa-miR-449b-5p	PAR-CLIP	23592263
MIRT462738	hsa-miR-4640-5p	PAR-CLIP	23592263
MIRT462737	hsa-miR-4726-5p	PAR-CLIP	23592263
MIRT462736	hsa-miR-3165	PAR-CLIP	23592263
MIRT462734	hsa-miR-3650	PAR-CLIP	23592263
MIRT462735	hsa-miR-4316	PAR-CLIP	23592263
MIRT462733	hsa-miR-1294	PAR-CLIP	23592263
MIRT462732	hsa-miR-7847-3p	PAR-CLIP	23592263
MIRT462731	hsa-miR-3691-5p	PAR-CLIP	23592263
MIRT462730	hsa-miR-3911	PAR-CLIP	23592263
MIRT462729	hsa-miR-1226-5p	PAR-CLIP	23592263
MIRT462728	hsa-miR-432-3p	PAR-CLIP	23592263
MIRT462727	hsa-miR-30b-3p	PAR-CLIP	23592263
MIRT954189	hsa-miR-1236	CLIP-seq
MIRT954190	hsa-miR-124	CLIP-seq
MIRT954191	hsa-miR-1321	CLIP-seq
MIRT954192	hsa-miR-1343	CLIP-seq
MIRT954193	hsa-miR-1910	CLIP-seq
MIRT954194	hsa-miR-3124-3p	CLIP-seq
MIRT954195	hsa-miR-3126-5p	CLIP-seq
MIRT954196	hsa-miR-3180-5p	CLIP-seq
MIRT954197	hsa-miR-335	CLIP-seq
MIRT954198	hsa-miR-34a	CLIP-seq
MIRT954199	hsa-miR-3682-3p	CLIP-seq
MIRT954200	hsa-miR-3923	CLIP-seq
MIRT954201	hsa-miR-3941	CLIP-seq
MIRT954202	hsa-miR-4266	CLIP-seq
MIRT954203	hsa-miR-4271	CLIP-seq
MIRT954204	hsa-miR-4274	CLIP-seq
MIRT954205	hsa-miR-4419a	CLIP-seq
MIRT954206	hsa-miR-4433	CLIP-seq
MIRT954207	hsa-miR-4435	CLIP-seq
MIRT954208	hsa-miR-4459	CLIP-seq
MIRT954209	hsa-miR-449b	CLIP-seq
MIRT954210	hsa-miR-4510	CLIP-seq
MIRT954211	hsa-miR-4514	CLIP-seq
MIRT954212	hsa-miR-466	CLIP-seq
MIRT954213	hsa-miR-4672	CLIP-seq
MIRT954214	hsa-miR-4692	CLIP-seq
MIRT954215	hsa-miR-4693-3p	CLIP-seq
MIRT954216	hsa-miR-4699-3p	CLIP-seq
MIRT954217	hsa-miR-4716-3p	CLIP-seq
MIRT954218	hsa-miR-4719	CLIP-seq
MIRT954219	hsa-miR-4722-5p	CLIP-seq
MIRT954220	hsa-miR-4725-3p	CLIP-seq
MIRT954221	hsa-miR-4731-3p	CLIP-seq
MIRT954222	hsa-miR-4739	CLIP-seq
MIRT954223	hsa-miR-4747-5p	CLIP-seq
MIRT954224	hsa-miR-4756-5p	CLIP-seq
MIRT954225	hsa-miR-4768-3p	CLIP-seq
MIRT954226	hsa-miR-4779	CLIP-seq
MIRT954227	hsa-miR-4801	CLIP-seq
MIRT954228	hsa-miR-506	CLIP-seq
MIRT954229	hsa-miR-548u	CLIP-seq
MIRT954230	hsa-miR-625	CLIP-seq
MIRT954231	hsa-miR-940	CLIP-seq
MIRT1982564	hsa-miR-1184	CLIP-seq
MIRT1982565	hsa-miR-1290	CLIP-seq
MIRT1982566	hsa-miR-147	CLIP-seq
MIRT1982567	hsa-miR-3190	CLIP-seq
MIRT954198	hsa-miR-34a	CLIP-seq
MIRT954209	hsa-miR-449b	CLIP-seq
MIRT1982568	hsa-miR-599	CLIP-seq
MIRT1982569	hsa-miR-644	CLIP-seq
MIRT1982564	hsa-miR-1184	CLIP-seq
MIRT2217436	hsa-miR-1207-3p	CLIP-seq
MIRT1982565	hsa-miR-1290	CLIP-seq
MIRT1982566	hsa-miR-147	CLIP-seq
MIRT954198	hsa-miR-34a	CLIP-seq
MIRT954209	hsa-miR-449b	CLIP-seq
MIRT1982568	hsa-miR-599	CLIP-seq
MIRT954189	hsa-miR-1236	CLIP-seq
MIRT954211	hsa-miR-4514	CLIP-seq
MIRT2387241	hsa-miR-4651	CLIP-seq
MIRT954214	hsa-miR-4692	CLIP-seq
MIRT2387242	hsa-miR-608	CLIP-seq
MIRT1982565	hsa-miR-1290	CLIP-seq
MIRT1982566	hsa-miR-147	CLIP-seq
MIRT1982568	hsa-miR-599	CLIP-seq
MIRT2521463	hsa-miR-1268	CLIP-seq
MIRT2521464	hsa-miR-1268b	CLIP-seq
MIRT2521465	hsa-miR-3176	CLIP-seq
MIRT2521466	hsa-miR-3922-3p	CLIP-seq
MIRT2521467	hsa-miR-4763-5p	CLIP-seq
MIRT2521468	hsa-miR-585	CLIP-seq
MIRT2521463	hsa-miR-1268	CLIP-seq
MIRT2521464	hsa-miR-1268b	CLIP-seq
MIRT2679837	hsa-miR-1972	CLIP-seq
MIRT2679838	hsa-miR-2355-5p	CLIP-seq
MIRT2679839	hsa-miR-2861	CLIP-seq
MIRT2521465	hsa-miR-3176	CLIP-seq
MIRT2679840	hsa-miR-3679-3p	CLIP-seq
MIRT2521466	hsa-miR-3922-3p	CLIP-seq
MIRT2679841	hsa-miR-4286	CLIP-seq
MIRT2679842	hsa-miR-4733-3p	CLIP-seq
MIRT2679843	hsa-miR-4757-5p	CLIP-seq
MIRT2521467	hsa-miR-4763-5p	CLIP-seq
MIRT2521468	hsa-miR-585	CLIP-seq

Show/Hide all (32)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001755	Process	Neural crest cell migration	IEA
GO:0005515	Function	Protein binding	IPI	9883737, 22279592, 32296183, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	8660976
GO:0007155	Process	Cell adhesion	TAS	8798744
GO:0007267	Process	Cell-cell signaling	TAS	8798744
GO:0007399	Process	Nervous system development	IEA
GO:0007411	Process	Axon guidance	IBA
GO:0007411	Process	Axon guidance	IEA
GO:0009880	Process	Embryonic pattern specification	IEA
GO:0009986	Component	Cell surface	IDA	12970314
GO:0016020	Component	Membrane	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0031295	Process	T cell costimulation	IEA
GO:0042098	Process	T cell proliferation	IEA
GO:0042102	Process	Positive regulation of T cell proliferation	IEA
GO:0042734	Component	Presynaptic membrane	IBA
GO:0045121	Component	Membrane raft	IEA
GO:0045202	Component	Synapse	ISS
GO:0046875	Function	Ephrin receptor binding	IBA
GO:0046875	Function	Ephrin receptor binding	IDA	23711177
GO:0046875	Function	Ephrin receptor binding	IEA
GO:0046875	Function	Ephrin receptor binding	TAS	8798744
GO:0048013	Process	Ephrin receptor signaling pathway	IBA
GO:0048013	Process	Ephrin receptor signaling pathway	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0098978	Component	Glutamatergic synapse	IBA
GO:2000785	Process	Regulation of autophagosome assembly	IDA	33280498

MIM	HGNC	e!Ensembl
300035	3226	ENSG00000090776

P98172

Protein name

Ephrin-B1 (EFL-3) (ELK ligand) (ELK-L) (EPH-related receptor tyrosine kinase ligand 2) (LERK-2) [Cleaved into: Ephrin-B1 C-terminal fragment (Ephrin-B1 CTF); Ephrin-B1 intracellular domain (Ephrin-B1 ICD)]

Protein function

Cell surface transmembrane ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development (PubMed:7973638, PubMed:8070404). Binding to

PDB

6THG

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00812	Ephrin	30 → 164	Ephrin	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed (PubMed:7973638, PubMed:8070404). Detected in both neuronal and non-neuronal tissues (PubMed:7973638, PubMed:8070404). Seems to have particularly strong expression in retina, sciatic nerve, heart and spinal cord (PubMe

Sequence

MARPGQRWLGKWLVAMVVWALCRLATPLAKNLEPVSWSSLNPKFLSGKGLVIYPKIGDKL
DIICPRAEAGRPYEYYKLYLVRPEQAAACSTVLDPNVLVTCNRPEQEIRFTIKFQEFSPN
YMGLEFKKHHDYYITSTSNGSLEGLENREGGVCRTRTMKIIMKVGQDPNAVTPEQLTTSR
PSKEADNTVKMATQAPGSRGSLGDSDGKHETVNQEEKSGPGASGGSSGDPDGFFNSKVAL
FAAVGAGCVIFLLIIIFLTVLLLKLRKRHRKHTQQRAAALSLSTLASPKGGSGTAGTEPS
DIIIPLRTTENNYCPHYEKVSGDYGHPVYIVQEMPPQSPANIYYKV

Sequence length

346

Interactions

View interactions

	KEGG		Reactome
	Axon guidance		EPH-Ephrin signaling EPHB-mediated forward signaling Ephrin signaling EPH-ephrin mediated repulsion of cells

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Craniofrontonasal syndrome	Pathogenic; Likely pathogenic	rs587777109, rs2147973166, rs2147976769, rs2147973177, rs2520012737, rs2520012797, rs879255545, rs104894796, rs104894801, rs28936069, rs28936070, rs28936071, rs28935170, rs104894802, rs104894803 View all (18 more)	RCV000087027 RCV001783192 RCV002249040 RCV002250863 RCV002467388 RCV002512506 RCV003226122 RCV000012473 RCV000012474 RCV000012475 RCV000012476 RCV000012477 RCV000012478 RCV000012479 RCV000012480 RCV000012481 RCV003316893 RCV003444084 RCV004555027 RCV004560500 RCV004594949 RCV000415481 RCV000415511 RCV000502211 RCV000503680 RCV000502264 RCV000500583 RCV000677734 RCV000984626 RCV001250921 RCV001174989 RCV001194644 RCV001263204 RCV001263202
EFNB1-related disorder	Likely pathogenic	rs1482772814	RCV003404510
Nonpapillary renal cell carcinoma	Pathogenic	rs2147976566	RCV005933657

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
See cases	Likely benign	rs758554867	RCV002252627

Show/Hide Text Mining Associations (39)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acrocephalosyndactylia	Associate	29215649, 30651579
Adenocarcinoma	Stimulate	12136247
Adenocarcinoma	Associate	30058095
Borderline Personality Disorder	Associate	25612291
Brain Neoplasms	Associate	34544797
Breast Neoplasms	Associate	22279592, 24240587, 26673618, 34544797
Capillary Malformation Arteriovenous Malformation	Associate	15124102
Cholangiocarcinoma	Associate	25012246
Colorectal Neoplasms	Associate	33525395
Craniofrontonasal dysplasia	Associate	15124102, 16685650, 20565770, 23335590, 28238796
Craniosynostoses	Associate	27884935
Developmental Disabilities	Associate	31088393
Disorders of Sex Development	Stimulate	12136247
Genetic Diseases X Linked	Associate	23335590
Glioblastoma	Associate	19728339
Hypoxia	Associate	30058095
Intellectual Disability	Associate	31088393
Leukemia	Associate	20061560
Lymphatic Metastasis	Stimulate	24240587
Lymphoproliferative Syndrome X Linked 2	Associate	20565770
Medulloblastoma	Associate	22723427, 25258252
Melanoma	Associate	35871080
Muenke Syndrome	Associate	29215649, 30651579
Muscular Dystrophy Duchenne	Associate	28877219
Neoplasm Metastasis	Associate	25012246
Neoplasms	Associate	12209731, 22279592, 25258252, 26673618
Neoplasms Germ Cell and Embryonal	Associate	18507018
Osteosarcoma	Associate	12209731
Ovarian Neoplasms	Associate	12960427
Pediatric Obesity	Associate	25612291
Plaque Atherosclerotic	Associate	21672356
Polyps	Inhibit	33525395
Precursor Cell Lymphoblastic Leukemia Lymphoma	Inhibit	35603962
Prostatic Neoplasms	Associate	30058095
Spinal Dysraphism	Associate	35741713
Stomach Neoplasms	Associate	12136247
Thrombosis	Associate	15994237
Thyroid Cancer Papillary	Associate	27986811
Triple Negative Breast Neoplasms	Stimulate	24240587

EFNB1 (ephrin B1)