EFNA2

ephrin A2, the group of Ephrins

Basic information

Region (hg38): 19:1285873-1301431

Previous symbols: [ "EPLG6" ]

Links

ENSG00000099617 ∙ NCBI:1943 ∙ OMIM:602756 ∙ HGNC:3222 ∙ Uniprot:O43921 ∙ 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 EFNA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFNA2 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						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in EFNA2

This is a list of pathogenic ClinVar variants found in the EFNA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1286175-C-T		not specified	Uncertain significance (Jun 30, 2022)
19-1286185-G-C		not specified	Uncertain significance (Jan 24, 2025)
19-1286232-C-A		not specified	Uncertain significance (Jul 22, 2024)
19-1286266-A-C		not specified	Uncertain significance (Apr 20, 2024)
19-1286268-T-A		not specified	Uncertain significance (Feb 15, 2023)
19-1295649-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-1295768-G-A		not specified	Uncertain significance (Apr 05, 2023)
19-1295774-C-T		not specified	Uncertain significance (Dec 14, 2024)
19-1298551-C-T		not specified	Uncertain significance (Jan 17, 2023)
19-1298566-A-G		not specified	Uncertain significance (Jul 12, 2022)
19-1298578-G-A		not specified	Uncertain significance (Jun 05, 2024)
19-1298614-C-A		not specified	Uncertain significance (Jan 23, 2024)
19-1299884-C-T		not specified	Likely benign (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFNA2	protein_coding	protein_coding	ENST00000215368	4	15278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0380	0.847	125535	0	7	125542	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	71	107	0.661	0.00000671	1336
Missense in Polyphen		17	35.046	0.48508		429
Synonymous	0.0645	51	51.6	0.989	0.00000377	429
Loss of Function	1.27	3	6.48	0.463	3.59e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000133	0.000122
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.0000555	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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. 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. With the EPHA2 receptor may play a role in bone remodeling through regulation of osteoclastogenesis and osteoblastogenesis (By similarity). {ECO:0000250}.
• 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;EPHA forward signaling (Consensus)

Recessive Scores

• pRec: 0.236

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.680
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efna2
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell-cell signaling;axon guidance;olfactory bulb development;osteoclast differentiation;bone remodeling;ephrin receptor signaling pathway
• Cellular component: plasma membrane;anchored component of membrane;neuromuscular junction;perikaryon
• Molecular function: protein binding;ephrin receptor binding