EPHA5

EPH receptor A5, the group of Sterile alpha motif domain containing|EPH receptors

Basic information

Region (hg38): 4:65319563-65670495

Links

ENSG00000145242 ∙ NCBI:2044 ∙ OMIM:600004 ∙ HGNC:3389 ∙ Uniprot:P54756 ∙ 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 EPHA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHA5 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					2	2
missense			35	2	1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	35	2	3

Variants in EPHA5

This is a list of pathogenic ClinVar variants found in the EPHA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-65324128-T-A		not specified	Uncertain significance (Apr 05, 2023)
4-65324131-C-T		not specified	Uncertain significance (Jun 18, 2021)
4-65324191-C-T		not specified	Uncertain significance (Mar 14, 2023)
4-65332106-G-C		not specified	Uncertain significance (Aug 03, 2022)
4-65335965-C-T		not specified	Uncertain significance (Jun 02, 2024)
4-65348065-T-A		not specified	Uncertain significance (Jan 08, 2024)
4-65348113-C-T		not specified	Uncertain significance (Jun 06, 2023)
4-65348188-T-C		not specified	Uncertain significance (May 05, 2023)
4-65353038-C-T			Benign (Jun 18, 2018)
4-65353065-C-A		not specified	Uncertain significance (Sep 01, 2021)
4-65365009-A-T			Benign (Oct 10, 2018)
4-65365052-G-A		not specified	Uncertain significance (Jan 30, 2024)
4-65365176-G-A		not specified	Uncertain significance (Apr 08, 2022)
4-65365187-A-G		not specified	Uncertain significance (Mar 30, 2024)
4-65365956-T-A		not specified	Uncertain significance (Oct 22, 2021)
4-65365965-A-T			Likely benign (Jun 01, 2018)
4-65365975-C-A		not specified	Uncertain significance (Aug 20, 2023)
4-65365981-A-G			Benign (Jul 15, 2018)
4-65367367-A-T		not specified	Uncertain significance (Mar 02, 2023)
4-65367417-C-T		not specified	Uncertain significance (Sep 20, 2023)
4-65377059-A-C		not specified	Uncertain significance (Feb 10, 2023)
4-65404419-C-T		Lung adenocarcinoma	Likely pathogenic (May 13, 2016)
4-65414389-C-G			Benign (May 18, 2018)
4-65414400-G-A		not specified	Uncertain significance (Mar 03, 2022)
4-65420545-C-T		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHA5	protein_coding	protein_coding	ENST00000273854	18	350933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000729	1.00	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	475	566	0.839	0.0000299	6763
Missense in Polyphen		200	283.69	0.70501		3401
Synonymous	-1.34	228	204	1.12	0.0000111	2009
Loss of Function	4.16	16	46.6	0.343	0.00000229	599

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000279	0.000279
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000238	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000892	0.0000879
Middle Eastern	0.000238	0.000217
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor tyrosine kinase which binds promiscuously GPI- anchored ephrin-A family ligands 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. Among GPI-anchored ephrin-A ligands, EFNA5 most probably constitutes the cognate/functional ligand for EPHA5. Functions as an axon guidance molecule during development and may be involved in the development of the retinotectal, entorhino- hippocampal and hippocamposeptal pathways. Together with EFNA5 plays also a role in synaptic plasticity in adult brain through regulation of synaptogenesis. In addition to its function in the nervous system, the interaction of EPHA5 with EFNA5 mediates communication between pancreatic islet cells to regulate glucose- stimulated insulin secretion (By similarity). {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Ephrin A reverse signaling;Axon guidance;EPHA forward signaling (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.594
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.49

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.737
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.588

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epha5
• 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)

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;peptidyl-tyrosine phosphorylation;cAMP-mediated signaling;hippocampus development;positive regulation of CREB transcription factor activity;regulation of actin cytoskeleton organization;regulation of GTPase activity;ephrin receptor signaling pathway;neuron development;regulation of insulin secretion involved in cellular response to glucose stimulus
• Cellular component: rough endoplasmic reticulum;plasma membrane;integral component of plasma membrane;external side of plasma membrane;axon;dendrite;neuron projection;neuronal cell body;receptor complex;perinuclear region of cytoplasm
• Molecular function: transmembrane receptor protein tyrosine kinase activity;ephrin receptor activity;GPI-linked ephrin receptor activity;transmembrane-ephrin receptor activity;ATP binding