EFNB2

ephrin B2, the group of Ephrins

Basic information

Region (hg38): 13:106489744-106535662

Previous symbols: [ "EPLG5" ]

Links

ENSG00000125266 ∙ NCBI:1948 ∙ OMIM:600527 ∙ HGNC:3227 ∙ Uniprot:P52799 ∙ 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 EFNB2 gene.

• Inborn genetic diseases (10 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFNB2 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				1		1
missense			10			10
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	1	10	1	0

Variants in EFNB2

This is a list of pathogenic ClinVar variants found in the EFNB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-106493117-C-T		not specified	Uncertain significance (Apr 27, 2022)
13-106493156-C-A		not specified	Uncertain significance (Oct 06, 2021)
13-106493244-C-T			Likely benign (Jul 25, 2018)
13-106493259-C-T		EFNB2-related disorder	Likely benign (Mar 27, 2019)
13-106493379-G-A		EFNB2-related disorder	Likely benign (Apr 04, 2019)
13-106493395-G-A		not specified	Uncertain significance (Jun 07, 2023)
13-106493399-G-A		not specified	Uncertain significance (Nov 15, 2021)
13-106493423-T-C		not specified	Uncertain significance (Jul 26, 2022)
13-106493436-C-T		EFNB2-related disorder	Likely benign (Jul 12, 2019)
13-106494949-C-T		not specified	Uncertain significance (Sep 01, 2021)
13-106494959-G-C		not specified	Uncertain significance (Feb 03, 2022)
13-106512521-A-T			Likely benign (Dec 31, 2019)
13-106512716-A-C		not specified	Likely pathogenic (Aug 22, 2019)
13-106512727-C-T		not specified	Uncertain significance (Aug 09, 2021)
13-106534851-C-A		EFNB2-related disorder	Likely benign (Feb 26, 2019)
13-106534949-C-T		not specified	Uncertain significance (Aug 02, 2022)
13-106534952-T-C		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFNB2	protein_coding	protein_coding	ENST00000245323	5	45384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0115	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	127	200	0.636	0.0000113	2177
Missense in Polyphen		36	81.325	0.44267		899
Synonymous	-0.645	94	86.4	1.09	0.00000592	647
Loss of Function	3.40	0	13.4	0.00	5.65e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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. Binds promiscuously Eph receptors 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. Binds to receptor tyrosine kinase including EPHA4, EPHA3 and EPHB4. Together with EPHB4 plays a central role in heart morphogenesis and angiogenesis through regulation of cell adhesion and cell migration. EPHB4-mediated forward signaling controls cellular repulsion and segregation from EFNB2-expressing cells. May play a role in constraining the orientation of longitudinally projecting axons. {ECO:0000269|PubMed:12734395}.
• Pathway: Axon guidance - Homo sapiens (human);Spinal Cord Injury;Developmental Biology;EPH-Ephrin signaling;Ephrin signaling;EGFR1;Ephrin B reverse signaling;Axon guidance;EPHB forward signaling (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.0354
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.457
• hipred: Y
• hipred_score: 0.853
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efnb2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; 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); normal phenotype; reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; hearing/vestibular/ear 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); digestive/alimentary phenotype; vision/eye phenotype

Zebrafish Information Network

• Gene name: efnb2a
• Affected structure: commissure of the tract of the commissure of the caudal tuberculum
• Phenotype tag: abnormal
• Phenotype quality: has extra parts of type

Gene ontology

• Biological process: lymph vessel development;cell migration involved in sprouting angiogenesis;cell adhesion;cell-cell signaling;axon guidance;positive regulation of cell population proliferation;anatomical structure morphogenesis;animal organ morphogenesis;negative regulation of keratinocyte proliferation;negative regulation of neuron projection development;peptidyl-tyrosine phosphorylation;T cell costimulation;viral entry into host cell;ephrin receptor signaling pathway;blood vessel morphogenesis;venous blood vessel morphogenesis;regulation of chemotaxis;nephric duct morphogenesis;presynapse assembly;regulation of postsynaptic membrane neurotransmitter receptor levels;regulation of postsynaptic neurotransmitter receptor internalization;positive regulation of neuron death;positive regulation of aorta morphogenesis;positive regulation of cardiac muscle cell differentiation
• Cellular component: plasma membrane;integral component of plasma membrane;focal adhesion;Schaffer collateral - CA1 synapse;glutamatergic synapse;integral component of presynaptic membrane;integral component of postsynaptic density membrane
• Molecular function: virus receptor activity;protein tyrosine kinase activity;protein binding;ephrin receptor binding