EFNA1

ephrin A1, the group of Ephrins

Basic information

Region (hg38): 1:155127876-155134899

Previous symbols: [ "TNFAIP4", "EPLG1" ]

Links

ENSG00000169242NCBI:1942OMIM:191164HGNC:3221Uniprot:P20827AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EFNA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFNA1 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
9
clinvar
1
clinvar
10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 9 0 1

Variants in EFNA1

This is a list of pathogenic ClinVar variants found in the EFNA1 region.

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

Position Type Phenotype Significance ClinVar
1-155131371-A-T not specified Uncertain significance (Feb 23, 2023)2488451
1-155131383-A-G not specified Uncertain significance (Jul 27, 2021)2239664
1-155131391-A-G not specified Uncertain significance (Mar 24, 2023)2524713
1-155131529-C-T not specified Uncertain significance (Feb 28, 2024)3087563
1-155131556-C-G not specified Uncertain significance (Oct 04, 2022)2316188
1-155133544-A-G not specified Uncertain significance (Mar 25, 2024)3274692
1-155133751-A-T Benign (Jan 09, 2019)1268289
1-155133752-C-A not specified Uncertain significance (May 11, 2022)2408945
1-155133771-C-T not specified Uncertain significance (Apr 08, 2022)2282662
1-155133973-T-C not specified Uncertain significance (Apr 22, 2022)2404086
1-155134023-T-C not specified Uncertain significance (Jan 16, 2024)3087565

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EFNA1protein_codingprotein_codingENST00000368407 57398
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4630.532125737071257440.0000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.833961220.7880.000006871351
Missense in Polyphen2345.1190.50976495
Synonymous1.043847.10.8070.00000259381
Loss of Function2.3429.990.2004.24e-7121

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006190.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003540.0000352
Middle Eastern0.000.00
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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. Plays an important role in angiogenesis and tumor neovascularization. The recruitment of VAV2, VAV3 and PI3-kinase p85 subunit by phosphorylated EPHA2 is critical for EFNA1-induced RAC1 GTPase activation and vascular endothelial cell migration and assembly. Exerts anti-oncogenic effects in tumor cells through activation and down-regulation of EPHA2. Activates EPHA2 by inducing tyrosine phosphorylation which leads to its internalization and degradation. Acts as a negative regulator in the tumorigenesis of gliomas by down-regulating EPHA2 and FAK. Can evoke collapse of embryonic neuronal growth cone and regulates dendritic spine morphogenesis. {ECO:0000269|PubMed:17332925, ECO:0000269|PubMed:18794797}.;
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);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Developmental Biology;EPH-Ephrin signaling;HIF-2-alpha transcription factor network;Axon guidance;Stabilization and expansion of the E-cadherin adherens junction;Arf6 signaling events;EPHA2 forward signaling;EPHA forward signaling (Consensus)

Recessive Scores

pRec
0.208

Intolerance Scores

loftool
0.147
rvis_EVS
0.26
rvis_percentile_EVS
70.06

Haploinsufficiency Scores

pHI
0.114
hipred
Y
hipred_score
0.701
ghis
0.488

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.978

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Efna1
Phenotype
muscle phenotype; skeleton 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); neoplasm;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;angiogenesis;positive regulation of protein phosphorylation;aortic valve morphogenesis;mitral valve morphogenesis;endocardial cushion to mesenchymal transition involved in heart valve formation;cell-cell signaling;axon guidance;negative regulation of epithelial to mesenchymal transition;notochord formation;cell migration;regulation of cell adhesion mediated by integrin;substrate adhesion-dependent cell spreading;negative regulation of MAPK cascade;positive regulation of MAPK cascade;regulation of blood vessel endothelial cell migration;regulation of angiogenesis;ephrin receptor signaling pathway;regulation of peptidyl-tyrosine phosphorylation;positive regulation of peptidyl-tyrosine phosphorylation;regulation of axonogenesis;protein stabilization;negative regulation of dendritic spine morphogenesis;positive regulation of protein tyrosine kinase activity;negative regulation of thymocyte apoptotic process;positive regulation of amyloid-beta formation;positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process;negative regulation of proteolysis involved in cellular protein catabolic process
Cellular component
extracellular region;plasma membrane;anchored component of plasma membrane
Molecular function
signaling receptor binding;protein binding;ephrin receptor binding