EFNA3
ephrin A3, the group of Ephrins
Basic information
Region (hg38): 1:155078837-155087538
Previous symbols: [ "EPLG3" ]
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 EFNA3 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 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 1 |
Variants in EFNA3
This is a list of pathogenic ClinVar variants found in the EFNA3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-155078994-T-A | not specified | Uncertain significance (Mar 04, 2024) | ||
| 1-155079068-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 1-155085095-C-T | not specified | Uncertain significance (Sep 12, 2023) | ||
| 1-155085133-C-G | not specified | Uncertain significance (Apr 12, 2023) | ||
| 1-155085167-T-G | not specified | Uncertain significance (Dec 20, 2021) | ||
| 1-155085192-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 1-155085201-G-C | not specified | Uncertain significance (Jul 12, 2022) | ||
| 1-155085221-G-A | not specified | Uncertain significance (May 26, 2024) | ||
| 1-155085311-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 1-155085361-T-G | Benign (Dec 31, 2019) | |||
| 1-155085937-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 1-155085940-C-A | not specified | Uncertain significance (Aug 22, 2023) | ||
| 1-155086196-A-G | not specified | Uncertain significance (May 17, 2023) | ||
| 1-155086481-C-T | not specified | Uncertain significance (Mar 17, 2023) | ||
| 1-155086482-G-A | not specified | Uncertain significance (Aug 07, 2023) | ||
| 1-155086493-C-T | not specified | Uncertain significance (Dec 19, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EFNA3 | protein_coding | protein_coding | ENST00000368408 | 5 | 23791 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.126 | 0.853 | 124798 | 0 | 3 | 124801 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.747 | 101 | 124 | 0.812 | 0.00000583 | 1516 |
| Missense in Polyphen | 33 | 55.704 | 0.59241 | 639 | ||
| Synonymous | 0.168 | 54 | 55.6 | 0.971 | 0.00000279 | 488 |
| Loss of Function | 1.99 | 3 | 9.67 | 0.310 | 4.10e-7 | 122 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000707 | 0.0000622 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000182 | 0.0000178 |
| 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 (By similarity). {ECO:0000250}.;
- 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);MicroRNAs in cancer - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Developmental Biology;EPH-Ephrin signaling;Axon guidance;EPHA forward signaling
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.190
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 66.82
Haploinsufficiency Scores
- pHI
- 0.436
- hipred
- N
- hipred_score
- 0.432
- ghis
- 0.531
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.971
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Efna3
- Phenotype
- growth/size/body region phenotype; 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); 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);
Gene ontology
- Biological process
- cell-cell signaling;axon guidance;negative regulation of angiogenesis;ephrin receptor signaling pathway;positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process
- Cellular component
- plasma membrane;anchored component of membrane;intrinsic component of plasma membrane
- Molecular function
- transmembrane-ephrin receptor activity;protein binding;ephrin receptor binding