EPHA1

EPH receptor A1, the group of Sterile alpha motif domain containing|EPH receptors

Basic information

Region (hg38): 7:143390289-143408856

Previous symbols: [ "EPHT", "EPHT1" ]

Links

ENSG00000146904 ∙ NCBI:2041 ∙ OMIM:179610 ∙ HGNC:3385 ∙ Uniprot:P21709 ∙ 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 EPHA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHA1 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	5	7
missense			71	8	1	80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding				2		2
Total	0	0	71	12	6

Variants in EPHA1

This is a list of pathogenic ClinVar variants found in the EPHA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-143390593-C-A		not specified	Uncertain significance (Dec 11, 2023)
7-143390600-T-G		not specified	Uncertain significance (Nov 19, 2022)
7-143391499-G-A			Benign (Dec 31, 2019)
7-143391504-C-T		not specified	Uncertain significance (Dec 19, 2023)
7-143391512-G-A		not specified	Uncertain significance (Mar 08, 2024)
7-143391665-G-A		not specified	Uncertain significance (Oct 06, 2021)
7-143391667-G-C		not specified	Uncertain significance (Mar 06, 2023)
7-143391687-G-A		not specified	Uncertain significance (Aug 10, 2021)
7-143391717-A-G		not specified	Likely benign (Feb 28, 2023)
7-143391731-G-A		not specified	Uncertain significance (Nov 12, 2021)
7-143391765-G-A		not specified	Uncertain significance (Dec 26, 2023)
7-143391770-G-A		not specified	Uncertain significance (Aug 01, 2022)
7-143393692-G-A		not specified	Uncertain significance (Jan 23, 2023)
7-143393695-C-T		not specified	Uncertain significance (Jun 11, 2024)
7-143393698-A-G		not specified	Uncertain significance (Aug 19, 2023)
7-143393751-G-A			Benign (Jul 22, 2018)
7-143393759-G-A		not specified	Uncertain significance (Mar 31, 2023)
7-143393764-G-C		not specified	Uncertain significance (Jun 18, 2024)
7-143393768-G-A		not specified	Uncertain significance (Apr 08, 2022)
7-143393836-C-T		not specified	Uncertain significance (May 26, 2024)
7-143394205-T-A		not specified	Uncertain significance (May 18, 2022)
7-143394271-C-T		not specified	Uncertain significance (Mar 27, 2023)
7-143394295-G-A		not specified	Uncertain significance (Jun 02, 2023)
7-143394295-G-C		not specified	Uncertain significance (Jan 22, 2024)
7-143394325-G-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHA1	protein_coding	protein_coding	ENST00000275815	18	18604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-23	0.0323	125561	2	185	125748	0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.222	574	589	0.974	0.0000371	6266
Missense in Polyphen		222	254.71	0.87158		2811
Synonymous	0.0113	238	238	0.999	0.0000144	2055
Loss of Function	1.29	41	50.9	0.805	0.00000305	505

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00149
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.000843	0.000816
Finnish	0.000190	0.000185
European (Non-Finnish)	0.000815	0.000800
Middle Eastern	0.000843	0.000816
South Asian	0.000621	0.000588
Other	0.00147	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor tyrosine kinase which binds promiscuously membrane-bound 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. Binds with a low affinity EFNA3 and EFNA4 and with a high affinity to EFNA1 which most probably constitutes its cognate/functional ligand. Upon activation by EFNA1 induces cell attachment to the extracellular matrix inhibiting cell spreading and motility through regulation of ILK and downstream RHOA and RAC. Plays also a role in angiogenesis and regulates cell proliferation. May play a role in apoptosis. {ECO:0000269|PubMed:17634955, ECO:0000269|PubMed:19118217, ECO:0000269|PubMed:20043122}.
• Pathway: Axon guidance - Homo sapiens (human);POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Developmental Biology;EPH-Ephrin signaling;POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;EGFR1;Transcriptional regulation of pluripotent stem cells;Axon guidance;EPHA forward signaling (Consensus)

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.565
• rvis_EVS: -0.9
• rvis_percentile_EVS: 10.17

Haploinsufficiency Scores

• pHI: 0.661
• hipred: Y
• hipred_score: 0.567
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.712

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epha1
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; immune system phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: angiogenesis;positive regulation of cell-matrix adhesion;negative regulation of protein kinase activity;cell surface receptor signaling pathway;transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;positive regulation of cell population proliferation;peptidyl-tyrosine phosphorylation;positive regulation of cell migration;negative regulation of cell migration;substrate adhesion-dependent cell spreading;somatic stem cell population maintenance;regulation of GTPase activity;positive regulation of angiogenesis;protein autophosphorylation;ephrin receptor signaling pathway;positive regulation of stress fiber assembly;activation of GTPase activity
• Cellular component: plasma membrane;integral component of plasma membrane;neuron projection;receptor complex
• Molecular function: protein kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane-ephrin receptor activity;ATP binding;protein kinase binding