EFNA1

ephrin A1, the group of Ephrins

Basic information

Region (hg38): 1:155127875-155134899

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

Links

ENSG00000169242 ∙ NCBI:1942 ∙ OMIM:191164 ∙ HGNC:3221 ∙ Uniprot:P20827 ∙ 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 EFNA1 gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

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			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	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)
1-155131383-A-G		not specified	Uncertain significance (Jul 27, 2021)
1-155131391-A-G		not specified	Uncertain significance (Mar 24, 2023)
1-155131529-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-155131556-C-G		not specified	Uncertain significance (Oct 04, 2022)
1-155133751-A-T			Benign (Jan 09, 2019)
1-155133752-C-A		not specified	Uncertain significance (May 11, 2022)
1-155133771-C-T		not specified	Uncertain significance (Apr 08, 2022)
1-155133973-T-C		not specified	Uncertain significance (Apr 22, 2022)
1-155134023-T-C		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFNA1	protein_coding	protein_coding	ENST00000368407	5	7398

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.463	0.532	125737	0	7	125744	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.833	96	122	0.788	0.00000687	1351
Missense in Polyphen		23	45.119	0.50976		495
Synonymous	1.04	38	47.1	0.807	0.00000259	381
Loss of Function	2.34	2	9.99	0.200	4.24e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000619	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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

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

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