EPHA6

EPH receptor A6, the group of EPH receptors|Sterile alpha motif domain containing

Basic information

Region (hg38): 3:96814581-97761532

Links

ENSG00000080224 ∙ NCBI:285220 ∙ OMIM:600066 ∙ HGNC:19296 ∙ Uniprot:Q9UF33 ∙ 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 EPHA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHA6 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	1	2
missense			56		1	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	1	2

Variants in EPHA6

This is a list of pathogenic ClinVar variants found in the EPHA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-96814652-G-A		not specified	Uncertain significance (Dec 01, 2022)
3-96814728-C-G		not specified	Uncertain significance (Jun 29, 2023)
3-96814759-C-T		not specified	Uncertain significance (Jun 27, 2023)
3-96814824-G-C		not specified	Uncertain significance (Aug 30, 2022)
3-96814837-A-G		not specified	Uncertain significance (May 05, 2022)
3-96814839-C-T			Benign (Mar 05, 2018)
3-96814840-C-G		not specified	Uncertain significance (Oct 26, 2022)
3-96814846-A-T		not specified	Uncertain significance (Feb 17, 2024)
3-96814865-A-G		not specified	Uncertain significance (Aug 10, 2021)
3-96814958-C-T		not specified	Uncertain significance (May 05, 2023)
3-96814970-C-T		not specified	Uncertain significance (Mar 02, 2023)
3-96814992-C-A		not specified	Uncertain significance (Oct 05, 2021)
3-96814997-C-T		not specified	Uncertain significance (Dec 01, 2022)
3-96815002-A-C		not specified	Uncertain significance (Oct 12, 2021)
3-96987441-C-T		not specified	Uncertain significance (Nov 17, 2022)
3-96987448-C-T		not specified	Uncertain significance (Nov 30, 2022)
3-96987519-A-G		not specified	Uncertain significance (Jul 12, 2022)
3-96987522-T-C		not specified	Uncertain significance (Nov 09, 2021)
3-96987556-C-T		not specified	Uncertain significance (Jul 21, 2021)
3-96987603-A-G		not specified	Uncertain significance (Jan 04, 2022)
3-96987687-G-A		not specified	Uncertain significance (Jul 11, 2023)
3-96987792-G-A		not specified	Uncertain significance (Jan 09, 2023)
3-96987796-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-96987834-G-A		not specified	Uncertain significance (Apr 25, 2023)
3-97226297-G-A		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHA6	protein_coding	protein_coding	ENST00000389672	18	937880

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.670	0.330	124726	0	20	124746	0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	505	609	0.829	0.0000311	7408
Missense in Polyphen		185	288	0.64237		3444
Synonymous	-1.11	233	212	1.10	0.0000108	2176
Loss of Function	5.05	10	47.5	0.210	0.00000252	614

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000252
Ashkenazi Jewish	0.00	0.00
East Asian	0.000170	0.000166
Finnish	0.0000479	0.0000464
European (Non-Finnish)	0.0000741	0.0000707
Middle Eastern	0.000170	0.000166
South Asian	0.0000982	0.0000980
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 (By similarity). {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Axon guidance;EPHA forward signaling (Consensus)

Intolerance Scores

• loftool: 0.440
• rvis_EVS: -0.77
• rvis_percentile_EVS: 13.15

Haploinsufficiency Scores

• pHI: 0.347
• hipred: Y
• hipred_score: 0.750
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.315

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epha6
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;biological_process;peptidyl-tyrosine phosphorylation;ephrin receptor signaling pathway
• Cellular component: cellular_component;nucleoplasm;plasma membrane;integral component of plasma membrane;neuron projection;receptor complex
• Molecular function: molecular_function;transmembrane receptor protein tyrosine kinase activity;transmembrane-ephrin receptor activity;ATP binding