EFNA5

ephrin A5, the group of Ephrins

Basic information

Region (hg38): 5:107376893-107670937

Previous symbols: [ "EPLG7" ]

Links

ENSG00000184349 ∙ NCBI:1946 ∙ OMIM:601535 ∙ HGNC:3225 ∙ Uniprot:P52803 ∙ 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 EFNA5 gene.

• Inborn genetic diseases (4 variants)

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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	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: gnomAD

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: 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. 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

• 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