EFNA4

ephrin A4, the group of Ephrins

Basic information

Region (hg38): 1:155063737-155069553

Previous symbols: [ "EPLG4" ]

Links

ENSG00000243364NCBI:1945OMIM:601380HGNC:3224Uniprot:P52798AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
4
clinvar
5
missense
15
clinvar
4
clinvar
19
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
2
clinvar
1
clinvar
3
Total 0 0 17 10 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)2336714
1-155063931-C-A Uncertain significance (May 12, 2023)2979191
1-155063954-G-A Likely benign (Oct 23, 2022)1916633
1-155063955-G-A Benign (Sep 01, 2022)1596612
1-155066749-G-C not specified Uncertain significance (Oct 13, 2023)2281424
1-155066794-C-T Likely benign (Aug 04, 2023)1554935
1-155066801-A-G not specified Uncertain significance (Mar 31, 2024)3274697
1-155066832-G-A Likely benign (Nov 15, 2023)2697653
1-155066845-A-G not specified Uncertain significance (May 30, 2023)2519275
1-155066891-G-A Uncertain significance (Oct 17, 2022)2074140
1-155066896-T-G not specified Uncertain significance (Mar 28, 2023)2530768
1-155066913-C-T Likely benign (Jul 29, 2023)3020185
1-155066941-T-C Uncertain significance (Dec 17, 2021)1957806
1-155066963-C-T Uncertain significance (May 25, 2022)2095429
1-155066965-C-A Likely benign (Nov 14, 2023)2061796
1-155066976-C-T Likely benign (Aug 24, 2023)2703624
1-155066988-C-T Benign/Likely benign (Nov 18, 2023)710307
1-155067002-C-G not specified Uncertain significance (Feb 28, 2023)2463192
1-155067030-G-A Likely benign (Jun 16, 2023)2968266
1-155067373-G-A Likely benign (Jan 31, 2024)2071464
1-155067396-G-T Uncertain significance (Sep 20, 2021)1362628
1-155067400-G-C Uncertain significance (Jun 10, 2023)3017647
1-155068854-G-T Uncertain significance (Jan 22, 2024)1900038
1-155068855-T-A Uncertain significance (Apr 08, 2022)2122848
1-155068883-C-T Uncertain significance (Jun 15, 2022)1990179

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EFNA4protein_codingprotein_codingENST00000427683 45823
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003500.6221257190201257390.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.760911140.7990.000006151288
Missense in Polyphen3242.4330.75413478
Synonymous0.2894547.50.9470.00000268445
Loss of Function0.65568.000.7504.00e-790

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001460.000146
Ashkenazi Jewish0.000.00
East Asian0.0001120.000109
Finnish0.000.00
European (Non-Finnish)0.00007990.0000791
Middle Eastern0.0001120.000109
South Asian0.0001050.0000980
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Efna4
Phenotype

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