EPHA10

EPH receptor A10, the group of EPH receptors|Sterile alpha motif domain containing

Basic information

Region (hg38): 1:37713879-37765133

Links

ENSG00000183317 ∙ NCBI:284656 ∙ OMIM:611123 ∙ HGNC:19987 ∙ Uniprot:Q5JZY3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal dominant 88 (Limited), mode of inheritance: AD
• hearing loss, autosomal dominant 88 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal dominant 88	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic	36048850

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPHA10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPHA10 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				3		3
missense			69	2	2	73
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	71	5	2

Variants in EPHA10

This is a list of pathogenic ClinVar variants found in the EPHA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37718434-T-C		not specified	Uncertain significance (Nov 07, 2022)
1-37718694-C-T		not specified	Uncertain significance (May 06, 2024)
1-37718709-G-A		not specified	Uncertain significance (Mar 20, 2024)
1-37718724-T-C		not specified	Uncertain significance (Jun 22, 2023)
1-37718730-C-G		not specified	Uncertain significance (Dec 22, 2023)
1-37718774-G-A			Likely benign (Mar 01, 2023)
1-37718794-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-37719429-A-G		not specified	Likely benign (Sep 01, 2021)
1-37719441-G-A		not specified	Uncertain significance (Apr 12, 2024)
1-37719487-G-C		not specified	Uncertain significance (Aug 02, 2022)
1-37719565-T-C		not specified	Uncertain significance (Dec 26, 2023)
1-37719567-G-A		not specified	Uncertain significance (Sep 28, 2021)
1-37719579-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-37719986-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-37720028-G-A		not specified	Uncertain significance (Jul 19, 2022)
1-37720031-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-37720052-G-A		not specified	Uncertain significance (Oct 21, 2021)
1-37720371-C-T		not specified	Uncertain significance (Jun 30, 2023)
1-37720376-C-G		not specified	Uncertain significance (Feb 02, 2022)
1-37720392-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-37720422-C-T		not specified	Uncertain significance (Dec 27, 2022)
1-37720442-C-A		not specified	Uncertain significance (Jul 20, 2021)
1-37720457-C-T		not specified	Uncertain significance (Oct 13, 2023)
1-37720815-T-C		not specified	Uncertain significance (Dec 26, 2023)
1-37720821-C-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPHA10	protein_coding	protein_coding	ENST00000373048	17	51254

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-26	0.000263	125532	1	215	125748	0.000859

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	512	573	0.893	0.0000373	6328
Missense in Polyphen		263	307.05	0.85654		3059
Synonymous	0.0547	255	256	0.996	0.0000180	2153
Loss of Function	0.0690	40	40.5	0.988	0.00000206	455

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00172	0.00165
Ashkenazi Jewish	0.000201	0.0000992
East Asian	0.00307	0.00299
Finnish	0.000105	0.0000924
European (Non-Finnish)	0.000719	0.000703
Middle Eastern	0.00307	0.00299
South Asian	0.000829	0.000817
Other	0.000826	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for members of the ephrin-A family. Binds to EFNA3, EFNA4 and EFNA5. {ECO:0000269|PubMed:15777695}.
• Pathway: Developmental Biology;EPH-Ephrin signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.753
• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.76

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.395
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epha10
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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