EPHB3

EPH receptor B3, the group of EPH receptors|Sterile alpha motif domain containing

Basic information

Region (hg38): 3:184561785-184582408

Previous symbols: [ "ETK2" ]

Links

ENSG00000182580 ∙ NCBI:2049 ∙ OMIM:601839 ∙ HGNC:3394 ∙ Uniprot:P54753 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPHB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHB3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	2	5
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	36	4	2

Variants in EPHB3

This is a list of pathogenic ClinVar variants found in the EPHB3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-184562243-G-A		not specified	Uncertain significance (Jun 10, 2024)
3-184562302-C-G		not specified	Uncertain significance (Mar 11, 2024)
3-184562342-G-A		not specified	Uncertain significance (Sep 01, 2021)
3-184571357-C-T		not specified	Uncertain significance (Jul 06, 2021)
3-184571363-C-T		not specified	Uncertain significance (May 27, 2022)
3-184572535-T-C		not specified	Uncertain significance (Feb 07, 2023)
3-184572571-G-A		not specified	Likely benign (May 18, 2023)
3-184572573-G-C		not specified	Uncertain significance (Aug 13, 2021)
3-184572580-G-C		not specified	Uncertain significance (Sep 26, 2023)
3-184572619-G-A		not specified	Uncertain significance (May 24, 2024)
3-184572768-A-T		not specified	Uncertain significance (Aug 30, 2021)
3-184572838-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-184573092-G-A		not specified	Uncertain significance (Jun 21, 2022)
3-184575916-G-A		not specified	Uncertain significance (Apr 09, 2024)
3-184575950-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-184576908-G-A		not specified	Uncertain significance (Jan 19, 2022)
3-184576916-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-184577000-C-T		not specified	Uncertain significance (Jan 05, 2022)
3-184577046-C-T		not specified	Uncertain significance (May 05, 2023)
3-184577117-G-A		not specified	Uncertain significance (May 03, 2023)
3-184577143-G-A			Benign (Jul 13, 2018)
3-184577412-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-184577420-C-T		not specified	Uncertain significance (Aug 15, 2023)
3-184577669-C-T			Likely benign (Jun 20, 2018)
3-184578010-C-T			Benign (Jan 25, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHB3	protein_coding	protein_coding	ENST00000330394	16	20626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.462	0.538	125730	0	13	125743	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	447	642	0.696	0.0000437	6450
Missense in Polyphen		147	279.71	0.52555		2736
Synonymous	-0.697	275	261	1.05	0.0000180	2052
Loss of Function	4.86	10	45.2	0.221	0.00000244	474

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.000147	0.000139
European (Non-Finnish)	0.0000539	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor tyrosine kinase which binds promiscuously transmembrane ephrin-B family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Generally has an overlapping and redundant function with EPHB2. Like EPHB2, functions in axon guidance during development regulating for instance the neurons forming the corpus callosum and the anterior commissure, 2 major interhemispheric connections between the temporal lobes of the cerebral cortex. In addition to its role in axon guidance plays also an important redundant role with other ephrin-B receptors in development and maturation of dendritic spines and the formation of excitatory synapses. Controls other aspects of development through regulation of cell migration and positioning. This includes angiogenesis, palate development and thymic epithelium development for instance. Forward and reverse signaling through the EFNB2/EPHB3 complex also regulate migration and adhesion of cells that tubularize the urethra and septate the cloaca. Finally, plays an important role in intestinal epithelium differentiation segregating progenitor from differentiated cells in the crypt. {ECO:0000269|PubMed:15536074}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Ephrin signaling;EGFR1;Axon guidance;EPHB forward signaling (Consensus)

Recessive Scores

• pRec: 0.228

Intolerance Scores

• loftool: 0.210
• rvis_EVS: -2.68
• rvis_percentile_EVS: 0.73

Haploinsufficiency Scores

• pHI: 0.421
• hipred: Y
• hipred_score: 0.756
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ephb3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; renal/urinary system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: ephb3b
• Affected structure: hepatoblast
• Phenotype tag: abnormal
• Phenotype quality: anterior orientation

Gene ontology

• Biological process: angiogenesis;urogenital system development;transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;axonal fasciculation;cell migration;peptidyl-tyrosine phosphorylation;central nervous system projection neuron axonogenesis;corpus callosum development;regulation of cell-cell adhesion;retinal ganglion cell axon guidance;substrate adhesion-dependent cell spreading;regulation of GTPase activity;protein autophosphorylation;ephrin receptor signaling pathway;thymus development;digestive tract morphogenesis;regulation of axonogenesis;positive regulation of synapse assembly;roof of mouth development;dendritic spine development;dendritic spine morphogenesis
• Cellular component: extracellular region;cytosol;plasma membrane;integral component of plasma membrane;dendrite;neuron projection;receptor complex
• Molecular function: protein tyrosine kinase activity;transmembrane receptor protein tyrosine kinase activity;ephrin receptor activity;transmembrane-ephrin receptor activity;ATP binding;axon guidance receptor activity