EPHA10

protein-coding

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

Gene summary

Ephrin receptors, the largest subfamily of receptor tyrosine kinases (RTKs), and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, shape, and mobility in neuronal and epithelial cells (Aasheim et al., 2005 [PubMed 15777695]). See MIM 179610 for additional background on Eph receptors and ephrins.[supplied by OMIM, Mar 2008]

MANE transcript

NM_001099439.2

Inheritance

ClinVar variants

U:181B:13

Top phenotype

Deafness, autosomal dominant 88

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr1:37,713,880-37,765,133

External References & Databases

Ensembl (ENSG00000183317)

Transcript & Mutation Effects

hg38 • Region Span ~51.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hearing loss, autosomal dominant 88LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0859527

Submitter: Ambry Genetics

hearing loss, autosomal dominant 88LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0859527

Submitter: Labcorp Genetics (formerly Invitae)

postlingual non-syndromic genetic hearing lossLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0016298

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Deafness, autosomal dominant 88AD

Manifestation: Audiologic/Otolaryngologic

Intervention: General

Rationale: 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

Refs: 36048850

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EPHA10 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 169

not providedTotal: 8

Hearing loss, autosomal dominant 88Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099439.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	8 clinvar		11
missense			170 clinvar	3 clinvar	2 clinvar	175
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	181	11	2	194

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099439.2	RefSeq	NP_001092909.1	17	MANE Select
ENST00000373048.9	Ensembl	ENSP00000362139.4	17	MANE Select
NM_173641.3	RefSeq	NP_775912.2	3	Standard
ENST00000319637.6	Ensembl	ENSP00000316395.6	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Developmental Biology
EPH-Ephrin signaling
Axon guidance

Biological Process

transmembrane receptor protein tyrosine kinase signaling pathway
axon guidance
biological_process
peptidyl-tyrosine phosphorylation
ephrin receptor signaling pathway

Molecular Function

transmembrane receptor protein tyrosine kinase activity
transmembrane-ephrin receptor activity
protein binding
ATP binding

Cellular Component

extracellular region
plasma membrane
integral component of plasma membrane
neuron projection
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373048
Coding exons: 17
Length: 51254
Individuals with no LoFs: 125532
Homozygous LoFs: 1
Heterozygous LoFs: 215
Defined: 125748
p: 0.000859

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.906	512	573	0.893	0.0000373	6328
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00043	rare
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.00020	0.000099	rare
East Asian	0.0031	0.0030	notable
Finnish	0.00010	0.000092	rare
European (Non-Finnish)	0.00072	0.00070	rare
South Asian	0.00083	0.00082	rare
Other	0.00083	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor for members of the ephrin-A family. Binds to EFNA3, EFNA4 and EFNA5. {ECO:0000269|PubMed:15777695}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.753
RVIS EVS: 1.08
RVIS percentile EVS: 91.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.731

Gene Damage Prediction

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