EFNB3
ephrin B3, the group of Ephrins
Basic information
Region (hg38): 17:7705202-7711372
Previous symbols: [ "EPLG8" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFNB3 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 | 0 | |||||
| missense | 16 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 1 |
Variants in EFNB3
This is a list of pathogenic ClinVar variants found in the EFNB3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-7705603-G-A | not specified | Uncertain significance (Mar 30, 2024) | ||
| 17-7705606-C-T | not specified | Uncertain significance (May 08, 2023) | ||
| 17-7705611-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 17-7705624-G-A | not specified | Uncertain significance (Dec 07, 2021) | ||
| 17-7705627-G-C | not specified | Uncertain significance (Aug 08, 2022) | ||
| 17-7705638-G-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 17-7708107-G-T | not specified | Uncertain significance (May 11, 2022) | ||
| 17-7708223-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
| 17-7708224-G-A | not specified | Uncertain significance (Oct 12, 2022) | ||
| 17-7708440-T-G | not specified | Uncertain significance (May 13, 2024) | ||
| 17-7708641-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 17-7708647-G-C | Benign (Oct 10, 2018) | |||
| 17-7708662-A-T | not specified | Uncertain significance (Apr 06, 2024) | ||
| 17-7709173-C-T | not specified | Uncertain significance (Jul 06, 2021) | ||
| 17-7709277-G-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 17-7709334-A-G | not specified | Uncertain significance (Jan 24, 2024) | ||
| 17-7709395-G-A | not specified | Uncertain significance (Oct 06, 2023) | ||
| 17-7709410-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 17-7709454-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 17-7709493-G-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 17-7709536-G-T | not specified | Uncertain significance (Aug 16, 2021) | ||
| 17-7709539-C-T | not specified | Uncertain significance (May 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EFNB3 | protein_coding | protein_coding | ENST00000226091 | 5 | 6177 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.321 | 0.676 | 125727 | 0 | 14 | 125741 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.57 | 136 | 198 | 0.686 | 0.0000117 | 2087 |
| Missense in Polyphen | 49 | 85.64 | 0.57216 | 891 | ||
| Synonymous | -0.680 | 89 | 81.2 | 1.10 | 0.00000421 | 775 |
| Loss of Function | 2.54 | 3 | 12.8 | 0.235 | 7.76e-7 | 135 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000982 | 0.0000979 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000188 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000371 | 0.000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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. May play a pivotal role in forebrain function. Binds to, and induce the collapse of, commissural axons/growth cones in vitro. May play a role in constraining the orientation of longitudinally projecting axons (By similarity). {ECO:0000250}.;
- Pathway
- Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Ephrin signaling;Axon guidance;EPHB forward signaling
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- 0.219
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 61.49
Haploinsufficiency Scores
- pHI
- 0.389
- hipred
- Y
- hipred_score
- 0.703
- ghis
- 0.533
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Efnb3
- Phenotype
- normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); cellular phenotype;
Gene ontology
- Biological process
- cell-cell signaling;nervous system development;axon guidance;adult walking behavior;axon choice point recognition;peptidyl-tyrosine phosphorylation;T cell costimulation;viral entry into host cell;ephrin receptor signaling pathway;negative regulation of axonogenesis;trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission
- Cellular component
- plasma membrane;integral component of plasma membrane;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;integral component of presynaptic membrane;integral component of postsynaptic density membrane
- Molecular function
- virus receptor activity;protein tyrosine kinase activity;transmembrane-ephrin receptor activity;ephrin receptor binding