EPHB1

EPH receptor B1, the group of EPH receptors|Sterile alpha motif domain containing

Basic information

Region (hg38): 3:134795259-135260467

Previous symbols: [ "EPHT2" ]

Links

ENSG00000154928 ∙ NCBI:2047 ∙ OMIM:600600 ∙ HGNC:3392 ∙ Uniprot:P54762 ∙ 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 EPHB1 gene.

• Inborn genetic diseases (31 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHB1 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	2

Variants in EPHB1

This is a list of pathogenic ClinVar variants found in the EPHB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-134795684-T-C		not specified	Uncertain significance (Jan 27, 2022)
3-134925838-G-A			Likely benign (Feb 01, 2023)
3-134925873-C-T		not specified	Uncertain significance (May 23, 2023)
3-134951516-G-A		not specified	Uncertain significance (Mar 07, 2024)
3-134951726-C-G		not specified	Uncertain significance (Jul 11, 2023)
3-134951770-C-T		not specified	Uncertain significance (Nov 12, 2021)
3-134951791-G-A		not specified	Uncertain significance (Aug 28, 2023)
3-134951837-C-A		not specified	Uncertain significance (Sep 27, 2021)
3-134951889-G-C		not specified	Uncertain significance (Jan 29, 2024)
3-134951912-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-134951923-A-G		not specified	Uncertain significance (Oct 06, 2021)
3-135106517-G-A		not specified	Uncertain significance (Feb 14, 2024)
3-135132843-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-135132937-C-A		not specified	Uncertain significance (Oct 20, 2023)
3-135132960-C-T		not specified	Uncertain significance (Sep 17, 2021)
3-135133004-T-C		not specified	Uncertain significance (Dec 12, 2023)
3-135133019-G-A		not specified	Uncertain significance (May 22, 2023)
3-135154166-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-135162049-G-A		not specified	Uncertain significance (Mar 23, 2022)
3-135162160-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-135166038-C-G		not specified	Uncertain significance (Aug 09, 2021)
3-135166038-C-T			Benign/Likely benign (Mar 01, 2023)
3-135166065-C-T			Benign (Feb 01, 2018)
3-135179860-G-C		not specified	Uncertain significance (Jun 16, 2023)
3-135192680-C-T		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHB1	protein_coding	protein_coding	ENST00000398015	16	662667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00150	125594	0	70	125664	0.000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	444	608	0.730	0.0000373	6468
Missense in Polyphen		124	240.83	0.5149		2631
Synonymous	-1.66	263	231	1.14	0.0000143	1945
Loss of Function	5.21	5	41.0	0.122	0.00000201	476

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00149	0.00136
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000109
Finnish	0.00104	0.000924
European (Non-Finnish)	0.000228	0.000202
Middle Eastern	0.000115	0.000109
South Asian	0.00	0.00
Other	0.000196	0.000163

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. Cognate/functional ephrin ligands for this receptor include EFNB1, EFNB2 and EFNB3. During nervous system development, regulates retinal axon guidance redirecting ipsilaterally ventrotemporal retinal ganglion cells axons at the optic chiasm midline. This probably requires repulsive interaction with EFNB2. In the adult nervous system together with EFNB3, regulates chemotaxis, proliferation and polarity of the hippocampus neural progenitors. 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 synapse formation. May also regulate angiogenesis. More generally, may play a role in targeted cell migration and adhesion. Upon activation by EFNB1 and probably other ephrin-B ligands activates the MAPK/ERK and the JNK signaling cascades to regulate cell migration and adhesion respectively. Involved in the maintenance of the pool of satellite cells (muscle stem cells) by promoting their self-renewal and reducing their activation and differentiation (By similarity). {ECO:0000250|UniProtKB:Q8CBF3, ECO:0000269|PubMed:12223469, ECO:0000269|PubMed:12925710, ECO:0000269|PubMed:18034775, ECO:0000269|PubMed:9430661, ECO:0000269|PubMed:9499402}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Ephrin signaling;EGFR1;Ephrin B reverse signaling;Axon guidance;EPHB forward signaling (Consensus)

Recessive Scores

• pRec: 0.227

Intolerance Scores

• loftool: 0.190
• rvis_EVS: -1.33
• rvis_percentile_EVS: 4.72

Haploinsufficiency Scores

• pHI: 0.820
• hipred: Y
• hipred_score: 0.786
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ephb1
• Phenotype: cellular 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); vision/eye phenotype

Gene ontology

• Biological process: angiogenesis;immunological synapse formation;transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;skeletal muscle satellite cell activation;peptidyl-tyrosine phosphorylation;optic nerve morphogenesis;central nervous system projection neuron axonogenesis;neurogenesis;establishment of cell polarity;retinal ganglion cell axon guidance;cell-substrate adhesion;regulation of JNK cascade;protein autophosphorylation;ephrin receptor signaling pathway;camera-type eye morphogenesis;modulation of chemical synaptic transmission;detection of temperature stimulus involved in sensory perception of pain;positive regulation of synapse assembly;cell chemotaxis;dendritic spine development;dendritic spine morphogenesis;neural precursor cell proliferation;regulation of ERK1 and ERK2 cascade;regulation of neuron death;negative regulation of skeletal muscle satellite cell proliferation;negative regulation of satellite cell differentiation
• Cellular component: extracellular region;endoplasmic reticulum;cytosol;plasma membrane;integral component of plasma membrane;axon;dendrite;early endosome membrane;filopodium tip;neuron projection;receptor complex;membrane raft;extracellular exosome;glutamatergic synapse
• Molecular function: protein tyrosine kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane-ephrin receptor activity;protein binding;ATP binding;axon guidance receptor activity;protein-containing complex binding