EFNA5
ephrin A5, the group of Ephrins
Basic information
Region (hg38): 5:107376894-107670937
Previous symbols: [ "EPLG7" ]
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 EFNA5 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in EFNA5
This is a list of pathogenic ClinVar variants found in the EFNA5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-107381368-C-T | not specified | Uncertain significance (Feb 01, 2023) | ||
| 5-107387288-T-C | not specified | Uncertain significance (Nov 17, 2023) | ||
| 5-107387312-C-T | not specified | Uncertain significance (Jan 03, 2022) | ||
| 5-107387757-C-G | not specified | Uncertain significance (Feb 28, 2024) | ||
| 5-107427319-G-A | not specified | Uncertain significance (Aug 22, 2023) | ||
| 5-107670538-T-C | not specified | Uncertain significance (May 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EFNA5 | protein_coding | protein_coding | ENST00000333274 | 5 | 294007 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.961 | 0.0394 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.52 | 84 | 133 | 0.631 | 0.00000741 | 1507 |
| Missense in Polyphen | 15 | 49.022 | 0.30598 | 558 | ||
| Synonymous | -0.173 | 55 | 53.4 | 1.03 | 0.00000327 | 424 |
| Loss of Function | 2.94 | 0 | 10.1 | 0.00 | 5.10e-7 | 125 |
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:
- Function
- FUNCTION: Cell surface GPI-bound 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. Induces compartmentalized signaling within a caveolae-like membrane microdomain when bound to the extracellular domain of its cognate receptor. This signaling event requires the activity of the Fyn tyrosine kinase. Activates the EPHA3 receptor to regulate cell-cell adhesion and cytoskeletal organization. With the receptor EPHA2 may regulate lens fiber cells shape and interactions and be important for lens transparency maintenance. May function actively to stimulate axon fasciculation. The interaction of EFNA5 with EPHA5 also mediates communication between pancreatic islet cells to regulate glucose-stimulated insulin secretion. Cognate/functional ligand for EPHA7, their interaction regulates brain development modulating cell-cell adhesion and repulsion. {ECO:0000269|PubMed:10601038, ECO:0000269|PubMed:11870224}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Axon guidance - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Vitamin D Receptor Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Splicing factor NOVA regulated synaptic proteins;PI3K-Akt Signaling Pathway;Developmental Biology;EPH-Ephrin signaling;Ephrin A reverse signaling;Axon guidance;EPHB forward signaling;EPHA forward signaling
(Consensus)
Recessive Scores
- pRec
- 0.357
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.356
- hipred
- Y
- hipred_score
- 0.851
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Efna5
- Phenotype
- craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive 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); growth/size/body region phenotype; vision/eye 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; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype;
Gene ontology
- Biological process
- positive regulation of protein phosphorylation;apoptotic process;activation of transmembrane receptor protein tyrosine kinase activity;nervous system development;axon guidance;regulation of cell-cell adhesion;regulation of cell morphogenesis;retinal ganglion cell axon guidance;regulation of actin cytoskeleton organization;regulation of GTPase activity;ephrin receptor signaling pathway;collateral sprouting;positive regulation of collateral sprouting;positive regulation of peptidyl-tyrosine phosphorylation;negative chemotaxis;regulation of focal adhesion assembly;positive regulation of synapse assembly;regulation of insulin secretion involved in cellular response to glucose stimulus;regulation of microtubule cytoskeleton organization;cellular response to follicle-stimulating hormone stimulus;synaptic membrane adhesion;negative regulation of substrate adhesion-dependent cell spreading;cellular response to forskolin
- Cellular component
- basement membrane;plasma membrane;caveola;adherens junction;anchored component of external side of plasma membrane;GABA-ergic synapse
- Molecular function
- neurotrophin TRKA receptor binding;neurotrophin TRKB receptor binding;neurotrophin TRKC receptor binding;protein binding;transmembrane receptor protein tyrosine kinase activator activity;chemorepellent activity;ephrin receptor binding