EFNA4

ephrin A4, the group of Ephrins

Basic information

Region (hg38): 1:155063737-155069553

Previous symbols: [ "EPLG4" ]

Links

ENSG00000243364 ∙ NCBI:1945 ∙ OMIM:601380 ∙ HGNC:3224 ∙ Uniprot:P52798 ∙ 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 EFNA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFNA4 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	4		5
missense			17	4		21
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding			1	4	1	6
Total	0	0	20	12	1

Variants in EFNA4

This is a list of pathogenic ClinVar variants found in the EFNA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155063928-T-A		not specified	Uncertain significance (Dec 19, 2022)
1-155063931-C-A			Uncertain significance (May 12, 2023)
1-155063943-G-A			Likely benign (Aug 14, 2024)
1-155063954-G-A			Likely benign (Oct 23, 2022)
1-155063955-G-A			Benign (Sep 01, 2022)
1-155066712-C-G			Likely benign (Oct 21, 2024)
1-155066717-G-A			Likely benign (Jun 03, 2024)
1-155066749-G-C		not specified	Uncertain significance (Feb 07, 2025)
1-155066794-C-T			Likely benign (Jan 06, 2025)
1-155066801-A-G		not specified	Uncertain significance (Mar 31, 2024)
1-155066827-G-A			Uncertain significance (Mar 23, 2024)
1-155066832-G-A			Likely benign (Oct 23, 2024)
1-155066845-A-G		not specified	Uncertain significance (May 30, 2023)
1-155066891-G-A		not specified	Uncertain significance (Jan 26, 2025)
1-155066894-C-A			Uncertain significance (Sep 24, 2024)
1-155066896-T-G		not specified	Uncertain significance (Mar 28, 2023)
1-155066913-C-T			Likely benign (Jul 29, 2023)
1-155066941-T-C			Uncertain significance (Dec 17, 2021)
1-155066952-T-C			Likely benign (Feb 14, 2024)
1-155066963-C-T			Uncertain significance (May 25, 2022)
1-155066965-C-A			Likely benign (Oct 23, 2024)
1-155066976-C-T			Likely benign (Oct 17, 2024)
1-155066988-C-T			Benign/Likely benign (Jan 30, 2025)
1-155066990-T-C		not specified	Uncertain significance (Mar 14, 2025)
1-155067002-C-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFNA4	protein_coding	protein_coding	ENST00000427683	4	5823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000350	0.622	125719	0	20	125739	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	91	114	0.799	0.00000615	1288
Missense in Polyphen		32	42.433	0.75413		478
Synonymous	0.289	45	47.5	0.947	0.00000268	445
Loss of Function	0.655	6	8.00	0.750	4.00e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000146	0.000146
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.000112	0.000109
South Asian	0.000105	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface GPI-bound ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development. Binds promiscuously Eph receptors residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. May play a role in the interaction between activated B-lymphocytes and dendritic cells in tonsils.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Axon guidance - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Developmental Biology;EPH-Ephrin signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.283
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.139
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efna4

Gene ontology

• Biological process: cell-cell signaling;axon guidance;osteoclast differentiation;bone remodeling;ephrin receptor signaling pathway
• Cellular component: extracellular region;plasma membrane;anchored component of membrane;intrinsic component of plasma membrane
• Molecular function: transmembrane-ephrin receptor activity;protein binding;ephrin receptor binding