EPHA7

EPH receptor A7, the group of EPH receptors|Sterile alpha motif domain containing

Basic information

Region (hg38): 6:93240019-93419687

Links

ENSG00000135333 ∙ NCBI:2045 ∙ OMIM:602190 ∙ HGNC:3390 ∙ Uniprot:Q15375 ∙ 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 EPHA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHA7 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	2	3
missense			44		2	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	44	1	5

Variants in EPHA7

This is a list of pathogenic ClinVar variants found in the EPHA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-93243433-T-C		not specified	Uncertain significance (Jan 02, 2024)
6-93243480-A-C		not specified	Uncertain significance (Jun 14, 2023)
6-93243540-C-A		not specified	Uncertain significance (Dec 15, 2022)
6-93245376-A-T		not specified	Uncertain significance (Aug 02, 2023)
6-93245413-T-A		not specified	Uncertain significance (Jun 06, 2023)
6-93245451-G-A		not specified	Uncertain significance (Sep 29, 2023)
6-93246795-C-G		not specified	Uncertain significance (Aug 09, 2021)
6-93246808-G-C		not specified	Uncertain significance (Nov 22, 2021)
6-93246897-T-G		not specified	Uncertain significance (Mar 14, 2023)
6-93246957-C-T		not specified	Uncertain significance (Sep 14, 2022)
6-93256008-C-A		not specified	Uncertain significance (Jan 08, 2024)
6-93258133-C-T			Benign (Dec 30, 2021)
6-93258195-T-C		not specified	Uncertain significance (Aug 30, 2022)
6-93258203-A-G		not specified	Uncertain significance (Aug 08, 2022)
6-93258245-G-C		not specified	Uncertain significance (Oct 17, 2023)
6-93258246-G-C		not specified	Uncertain significance (Feb 22, 2023)
6-93258258-G-T		not specified	Uncertain significance (Jan 31, 2023)
6-93258275-C-A		not specified	Uncertain significance (May 18, 2023)
6-93259360-C-A		not specified	Uncertain significance (Dec 15, 2022)
6-93264637-T-C		not specified	Uncertain significance (Sep 13, 2023)
6-93269533-T-C		not specified	Uncertain significance (Dec 14, 2023)
6-93269543-A-G		not specified	Uncertain significance (Jan 26, 2023)
6-93269563-C-T			Uncertain significance (Jan 26, 2022)
6-93269568-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
6-93269608-G-A		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHA7	protein_coding	protein_coding	ENST00000369303	17	179528

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.80e-7	125738	0	7	125745	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	385	541	0.711	0.0000268	6560
Missense in Polyphen		134	221.84	0.60405		2739
Synonymous	-0.384	193	186	1.04	0.00000946	1879
Loss of Function	6.24	2	49.3	0.0406	0.00000249	599

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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 is a cognate/functional ligand for EPHA7 and their interaction regulates brain development modulating cell-cell adhesion and repulsion. Has a repellent activity on axons and is for instance involved in the guidance of corticothalamic axons and in the proper topographic mapping of retinal axons to the colliculus. May also regulate brain development through a caspase(CASP3)-dependent proapoptotic activity. Forward signaling may result in activation of components of the ERK signaling pathway including MAP2K1, MAP2K2, MAPK1 AND MAPK3 which are phosphorylated upon activation of EPHA7. {ECO:0000269|PubMed:17726105}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Axon guidance;EPHA forward signaling (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.223
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.85

Haploinsufficiency Scores

• pHI: 0.898
• hipred: Y
• hipred_score: 0.793
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epha7
• 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: apoptotic process;transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;brain development;phosphorylation;peptidyl-tyrosine phosphorylation;regulation of cell-cell adhesion;retinal ganglion cell axon guidance;regulation of protein autophosphorylation;regulation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of neuron apoptotic process;ephrin receptor signaling pathway;negative regulation of collateral sprouting;branching morphogenesis of a nerve;regulation of peptidyl-tyrosine phosphorylation;negative chemotaxis;negative regulation of synapse assembly;regulation of ERK1 and ERK2 cascade;nephric duct morphogenesis;regulation of postsynapse organization
• Cellular component: plasma membrane;integral component of plasma membrane;dendrite;neuromuscular junction;neuron projection;neuronal cell body;receptor complex;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: protein tyrosine kinase activity;transmembrane receptor protein tyrosine kinase activity;GPI-linked ephrin receptor activity;transmembrane-ephrin receptor activity;protein binding;ATP binding;axon guidance receptor activity;chemorepellent activity;ephrin receptor binding