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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	253738
Gene name	EBF transcription factor 3
Gene symbol	EBF3
Synonyms (NCBI Gene)	COE3EBF-3HADDSO/E-2OE-2
Chromosome	10
Chromosome location	10q26.3
Summary	This gene encodes a member of the early B-cell factor (EBF) family of DNA binding transcription factors. EBF proteins are involved in B-cell differentiation, bone development and neurogenesis, and may also function as tumor suppressors. The encoded protei

Show/Hide all (37)

SNP ID	Visualize variation	Clinical significance	Consequence
rs778076484	G>C,T	Pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant, non coding transcript variant, missense variant
rs779003155	G>A,T	Pathogenic	Synonymous variant, non coding transcript variant, coding sequence variant, missense variant
rs869312668	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant, genic upstream transcript variant
rs886040976	T>C	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1057519389	C>A,G,T	Likely-pathogenic, pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1057519437	C>T	Pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1057519518	T>C	Pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1057519519	T>C	Pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1057519520	C>A,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant, synonymous variant
rs1057519521	TCTC>-	Pathogenic	Genic upstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1057519522	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1057524002	G>A	Pathogenic	Genic upstream transcript variant, non coding transcript variant, stop gained, coding sequence variant
rs1064794961	GTACTGCTGGGGA>-	Pathogenic	Frameshift variant, non coding transcript variant, intron variant, coding sequence variant
rs1064796766	A>C	Pathogenic	Genic upstream transcript variant, non coding transcript variant, stop gained, coding sequence variant
rs1085307482	CT>-	Pathogenic	Genic upstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1131692258	C>T	Pathogenic	Splice acceptor variant, genic upstream transcript variant
rs1131692259	C>-	Pathogenic	Genic upstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1131692260	G>T	Likely-pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1131692261	C>T	Likely-pathogenic, pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1131692262	T>G	Likely-pathogenic	Genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1172303286	G>A,T	Likely-pathogenic	Stop gained, non coding transcript variant, missense variant, coding sequence variant
rs1554902885	T>C	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1554904330	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1554934855	C>T	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs1554935456	->ATCTCGTGG	Pathogenic	Non coding transcript variant, inframe insertion, coding sequence variant, genic upstream transcript variant
rs1554935464	G>A	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs1554935484	->G	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, genic upstream transcript variant
rs1554937243	C>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, genic upstream transcript variant
rs1554937249	CCG>TCA	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, genic upstream transcript variant
rs1564816319	G>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1564840008	->A	Likely-pathogenic	Non coding transcript variant, intron variant, coding sequence variant, frameshift variant
rs1564927062	CA>AG	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs1589745620	C>-,CC	Pathogenic, not-provided	Frameshift variant, coding sequence variant, intron variant, non coding transcript variant
rs1589767274	C>T	Pathogenic	Splice donor variant
rs1589767433	AGAA>-	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1589962586	C>T	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs1589974634	C>A	Pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, stop gained

Show/Hide all (86)

miRTarBase ID	miRNA	Experiments
MIRT951373	hsa-miR-1283	CLIP-seq
MIRT951374	hsa-miR-197	CLIP-seq
MIRT951375	hsa-miR-299-3p	CLIP-seq
MIRT951376	hsa-miR-30a	CLIP-seq
MIRT951377	hsa-miR-30b	CLIP-seq
MIRT951378	hsa-miR-30c	CLIP-seq
MIRT951379	hsa-miR-30d	CLIP-seq
MIRT951380	hsa-miR-30e	CLIP-seq
MIRT951381	hsa-miR-3162-5p	CLIP-seq
MIRT951382	hsa-miR-3613-3p	CLIP-seq
MIRT951383	hsa-miR-3618	CLIP-seq
MIRT951384	hsa-miR-4491	CLIP-seq
MIRT951385	hsa-miR-4657	CLIP-seq
MIRT951386	hsa-miR-590-3p	CLIP-seq
MIRT1548129	hsa-miR-3153	CLIP-seq
MIRT1548130	hsa-miR-4668-5p	CLIP-seq
MIRT1981813	hsa-miR-145	CLIP-seq
MIRT1981814	hsa-miR-3684	CLIP-seq
MIRT1981815	hsa-miR-4788	CLIP-seq
MIRT1981816	hsa-miR-505	CLIP-seq
MIRT1981817	hsa-miR-548k	CLIP-seq
MIRT1981818	hsa-miR-548n	CLIP-seq
MIRT1981819	hsa-miR-548t	CLIP-seq
MIRT2216663	hsa-miR-1271	CLIP-seq
MIRT2216664	hsa-miR-182	CLIP-seq
MIRT2216665	hsa-miR-3591-3p	CLIP-seq
MIRT2216666	hsa-miR-4470	CLIP-seq
MIRT2216667	hsa-miR-4719	CLIP-seq
MIRT2216668	hsa-miR-518a-5p	CLIP-seq
MIRT2216669	hsa-miR-527	CLIP-seq
MIRT2216670	hsa-miR-96	CLIP-seq
MIRT2387201	hsa-miR-218	CLIP-seq
MIRT2387202	hsa-miR-636	CLIP-seq
MIRT2448635	hsa-miR-2392	CLIP-seq
MIRT2448636	hsa-miR-3688-3p	CLIP-seq
MIRT2448637	hsa-miR-3978	CLIP-seq
MIRT2520599	hsa-miR-1256	CLIP-seq
MIRT2520600	hsa-miR-1343	CLIP-seq
MIRT2520601	hsa-miR-2355-3p	CLIP-seq
MIRT2448635	hsa-miR-2392	CLIP-seq
MIRT951375	hsa-miR-299-3p	CLIP-seq
MIRT2520602	hsa-miR-3144-5p	CLIP-seq
MIRT2520603	hsa-miR-3191	CLIP-seq
MIRT2520604	hsa-miR-33a	CLIP-seq
MIRT2520605	hsa-miR-33b	CLIP-seq
MIRT2520606	hsa-miR-3616-5p	CLIP-seq
MIRT2520607	hsa-miR-3647-5p	CLIP-seq
MIRT2448636	hsa-miR-3688-3p	CLIP-seq
MIRT2520608	hsa-miR-382	CLIP-seq
MIRT2520609	hsa-miR-3945	CLIP-seq
MIRT2448637	hsa-miR-3978	CLIP-seq
MIRT2520610	hsa-miR-4253	CLIP-seq
MIRT2520611	hsa-miR-4265	CLIP-seq
MIRT2520612	hsa-miR-4296	CLIP-seq
MIRT2520613	hsa-miR-4322	CLIP-seq
MIRT2520614	hsa-miR-4417	CLIP-seq
MIRT2520615	hsa-miR-4646-3p	CLIP-seq
MIRT2520616	hsa-miR-4652-3p	CLIP-seq
MIRT2520617	hsa-miR-4652-5p	CLIP-seq
MIRT2520618	hsa-miR-4667-5p	CLIP-seq
MIRT2520619	hsa-miR-4700-5p	CLIP-seq
MIRT2520620	hsa-miR-4775	CLIP-seq
MIRT2520621	hsa-miR-4778-5p	CLIP-seq
MIRT2520622	hsa-miR-4795-5p	CLIP-seq
MIRT2520623	hsa-miR-573	CLIP-seq
MIRT951386	hsa-miR-590-3p	CLIP-seq
MIRT2520624	hsa-miR-653	CLIP-seq
MIRT2520600	hsa-miR-1343	CLIP-seq
MIRT2520601	hsa-miR-2355-3p	CLIP-seq
MIRT2448635	hsa-miR-2392	CLIP-seq
MIRT2520602	hsa-miR-3144-5p	CLIP-seq
MIRT2520603	hsa-miR-3191	CLIP-seq
MIRT2520604	hsa-miR-33a	CLIP-seq
MIRT2520605	hsa-miR-33b	CLIP-seq
MIRT2448636	hsa-miR-3688-3p	CLIP-seq
MIRT2520608	hsa-miR-382	CLIP-seq
MIRT2448637	hsa-miR-3978	CLIP-seq
MIRT2520615	hsa-miR-4646-3p	CLIP-seq
MIRT2520616	hsa-miR-4652-3p	CLIP-seq
MIRT2520617	hsa-miR-4652-5p	CLIP-seq
MIRT2520618	hsa-miR-4667-5p	CLIP-seq
MIRT2520619	hsa-miR-4700-5p	CLIP-seq
MIRT2520620	hsa-miR-4775	CLIP-seq
MIRT2520621	hsa-miR-4778-5p	CLIP-seq
MIRT951386	hsa-miR-590-3p	CLIP-seq
MIRT2520624	hsa-miR-653	CLIP-seq

Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IDA	28017373
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0008270	Function	Zinc ion binding	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IMP	28017370, 28017372, 28017373
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
607407	19087	ENSG00000108001

Q9H4W6

Protein name

Transcription factor COE3 (Early B-cell factor 3) (EBF-3) (Olf-1/EBF-like 2) (O/E-2) (OE-2)

Protein function

Transcriptional activator (PubMed:28017370, PubMed:28017372, PubMed:28017373). Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). {ECO:0000250|UniProtKB:Q07802, ECO:0000269|PubMed:28017370, ECO:0000269|PubMe

PDB

3MUJ , 3N50

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF16422	COE1_DBD	17 → 247	Transcription factor COE1 DNA-binding domain	Domain
PF01833	TIG	263 → 345	IPT/TIG domain	Domain
PF16423	COE1_HLH	348 → 391	Transcription factor COE1 helix-loop-helix domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in brain. {ECO:0000269|PubMed:12355068}.

Sequence

MFGIQENIPRGGTTMKEEPLGSGMNPVRSWMHTAGVVDANTAAQSGVGLARAHFEKQPPS
NLRKSNFFHFVLALYDRQGQPVEIERTAFVDFVEKEKEPNNEKTNNGIHYKLQLLYSNGV
RTEQDLYVRLIDSMTKQAIVYEGQDKNPEMCRVLLTHEIMCSRCCDKKSCGNRNETPSDP
VIIDRFFLKFFLKCNQNCLKNAGNPRDMRRFQVVVSTTVNVDGHVLAVSDNMFVHNNSKH
GRRARRLDPSEGTAPSYLENATPCIKAISPSEGWTTGGATVIIIGDNFFDGLQVVFGTML
VWSELITPHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGAPGRFVYTALNEPTIDYGFQRL
QKVIPRHPGDPERLPKEVLLKRAADLVEALYGMPHNNQEIILKRAADIAEALYSVPRNHN
QIPTLGNNPAHTGMMGVNSFSSQLAVNVSETSQANDQVGYSRNTSSVSPRGYVPSSTPQQ
SNYNTVSTSMNGYGSGAMASLGVPGSPGFLNGSSANSPYGIVPSSPTMAASSVTLPSNCS
STHGIFSFSPANVISAVKQKSAFAPVVRPQASPPPSCTSANGNGLQAMSGLVVPPM

Sequence length

596

Interactions

View interactions

143

Show/Hide Causal Diseases (17)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ataxia	Pathogenic	rs1057519389	RCV000417075 RCV000417073
Autism spectrum disorder	Pathogenic	rs2493681198	RCV003127425
Broad-based gait	Pathogenic	rs1057519437	RCV000416467
Developmental regression	Pathogenic	rs1057519437	RCV000416467
EBF3-related disorder	Likely pathogenic; Pathogenic	rs2494042487, rs2493684497, rs1564816319	RCV004531571 RCV004528777 RCV002221583
Expressive language delay	Pathogenic	rs1057519389	RCV000417075 RCV000417073
Generalized hypotonia	Pathogenic	rs1057519437	RCV000416467
Global developmental delay	Pathogenic	rs1057519389	RCV000417075 RCV000417073
Hypotonia	Pathogenic	rs1057519389	RCV000417075 RCV000417073
Hypotonia, ataxia, and delayed development syndrome	Likely pathogenic; Pathogenic	rs1268207836, rs1859684125, rs2134129705, rs2134129845, rs2134659512, rs2134610864, rs1484783852, rs2134659091, rs2134610480, rs2134610777, rs2134129924, rs2134659487, rs2134108087, rs1057519092, rs2134129636 View all (34 more)	RCV001331434 RCV001334634 RCV001594472 RCV001638191 RCV001706809 RCV001706846 RCV001724782 RCV001754540 RCV001775279 RCV001843847 RCV002249037 RCV002249038 RCV002273229 RCV002275710 RCV002275711 RCV002275712 RCV002285209 RCV002290097 RCV002508853 RCV005255485 RCV000416981 RCV000416975 RCV000416944 RCV003315125 RCV003337792 RCV003459152 RCV003883345 RCV003990269 RCV004579664 RCV000415489 RCV001526827 RCV000417009 RCV000416941 RCV000417002 RCV000417019 RCV000416948 RCV000416978 RCV000417012 RCV004760527 RCV001267692 RCV001526828 RCV003139699 RCV000656407 RCV000678910 RCV001594405 RCV000853316 RCV000988458 RCV002051909 RCV001027864 RCV001028017 RCV001252229 RCV001254071 RCV001283832
Intellectual disability	Pathogenic	rs1057519389, rs1131692258	RCV000417075 RCV000417073 RCV005625639
Isolated Pierre-Robin syndrome	Pathogenic	rs1057519389	RCV000663416
Neurodevelopmental disorder	Pathogenic	rs1057519522	RCV000505244
Neurogenic bladder	Pathogenic	rs1057519437	RCV000416467
Oromandibular-limb hypogenesis spectrum	Likely pathogenic	rs886040976	RCV000258066
Renal tubular dysgenesis	Pathogenic	rs1057519437	RCV000416467
See cases	Pathogenic; Likely pathogenic	rs2134658539, rs2134076706, rs779003155	RCV001420194 RCV002252832 RCV004797808

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	rs758276315	RCV004560246
Intellectual disability, X-linked 102	Conflicting classifications of pathogenicity	rs2493747181	RCV005861323

Show/Hide Text Mining Associations (40)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alcohol Related Disorders	Associate	28017372
Arthritis Rheumatoid	Associate	23456299
Ataxia	Associate	28017372, 28017373, 28487885, 29162653, 34999443
Autistic Disorder	Associate	29162653, 34256850
Bicornuate Uterus	Associate	28487885
Central Nervous System Vascular Malformations	Associate	28017372
Cerebellar Ataxia	Associate	28017370
Cognition Disorders	Associate	34999443
Colorectal Neoplasms	Associate	31383000
Delayed Cranial Ossification due to CBFB Haploinsufficiency	Associate	29162653
Developmental Disabilities	Associate	28017370, 28017372, 28017373, 28487885, 29162653, 34256850, 34999443
Esophageal Neoplasms	Associate	29750239
Esophageal Squamous Cell Carcinoma	Associate	29750239
Facial Dysmorphism with Multiple Malformations	Associate	28017370, 28017373, 28487885
Glioblastoma	Associate	25609158
Growth Disorders	Associate	29162653
Intellectual Disability	Associate	28017370, 28017372, 28017373, 28487885, 29162653
Language Development Disorders	Associate	28017373, 28487885
Leukemia Lymphocytic Chronic B Cell	Inhibit	33837967
Leukemia Myeloid Acute	Associate	25609158, 37271497
Lissencephaly X Linked 2	Associate	28017372
Melanoma	Associate	28030832, 29522175, 31383000
Melanoma Cutaneous Malignant	Associate	29522175
Mental Disorders	Associate	33335013
Muscle Hypotonia	Associate	28017372, 29162653, 34256850
Nasopharyngeal Carcinoma	Associate	34906623
Neoplasm Metastasis	Associate	28030832, 31383000
Neoplasm Metastasis	Inhibit	29750239
Neoplasm Metastasis	Stimulate	34906623
Neoplasms	Associate	14514668, 31383000
Neoplasms	Inhibit	25609158, 29522175
Nervous System Malformations	Associate	28017372
Osteoarthritis	Associate	23456299
Pancreatic Intraductal Neoplasms	Associate	22173550
Retinal Dysplasia	Associate	22173550
Speech Disorders	Associate	28017372
Strabismus	Associate	28017370
Thakker Donnai syndrome	Associate	29162653
Urogenital Abnormalities	Associate	28017372
Vesico Ureteral Reflux	Associate	28017370

EBF3 (EBF transcription factor 3)