EFNB1

ephrin B1, the group of Ephrins

Basic information

Region (hg38): X:68829021-68842160

Previous symbols: [ "EPLG2", "CFNS" ]

Links

ENSG00000090776NCBI:1947OMIM:300035HGNC:3226Uniprot:P98172AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • craniofrontonasal syndrome (Supportive), mode of inheritance: XL
  • craniofrontonasal syndrome (Definitive), mode of inheritance: XL
  • craniofrontonasal syndrome (Definitive), mode of inheritance: XL
  • craniofrontonasal syndrome (Strong), mode of inheritance: XL
  • craniofrontonasal syndrome (Strong), mode of inheritance: XL
  • craniofrontonasal syndrome (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Craniofrontonasal dysplasiaXLGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal15166289; 15124102; 15959873; 16639408; 17941886; 18627045; 20734337; 21385071; 23509643

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EFNB1 gene.

  • not_provided (104 variants)
  • Craniofrontonasal_syndrome (46 variants)
  • Inborn_genetic_diseases (38 variants)
  • EFNB1-related_disorder (7 variants)
  • not_specified (1 variants)
  • See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFNB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004429.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
18
clinvar
2
clinvar
21
missense
11
clinvar
17
clinvar
70
clinvar
4
clinvar
2
clinvar
104
nonsense
13
clinvar
3
clinvar
16
start loss
1
1
frameshift
13
clinvar
6
clinvar
2
clinvar
21
splice donor/acceptor (+/-2bp)
3
clinvar
4
clinvar
7
Total 42 30 72 22 4

Highest pathogenic variant AF is 9.1527403e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EFNB1protein_codingprotein_codingENST00000204961 513151
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9330.067200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.591001560.6410.00001322241
Missense in Polyphen3164.0370.4841934
Synonymous0.2636567.80.9590.00000584712
Loss of Function2.7108.580.006.16e-7148

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds to the receptor tyrosine kinases EPHB1 and EPHA1. Binds to, and induce the collapse of, commissural axons/growth cones in vitro. May play a role in constraining the orientation of longitudinally projecting axons (By similarity). {ECO:0000250}.;
Disease
DISEASE: Craniofrontonasal syndrome (CFNS) [MIM:304110]: X-linked inherited syndrome characterized by hypertelorism, coronal synostosis with brachycephaly, downslanting palpebral fissures, clefting of the nasal tip, joint anomalies, longitudinally grooved fingernails and other digital anomalies. {ECO:0000269|PubMed:15124102, ECO:0000269|PubMed:15166289, ECO:0000269|PubMed:15959873}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Axon guidance - Homo sapiens (human);Developmental Biology;EPH-Ephrin signaling;Ephrin signaling;Ephrin B reverse signaling;Axon guidance;EPHB forward signaling (Consensus)

Recessive Scores

pRec
0.371

Intolerance Scores

loftool
rvis_EVS
0.22
rvis_percentile_EVS
68.13

Haploinsufficiency Scores

pHI
0.268
hipred
Y
hipred_score
0.645
ghis
0.485

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.862

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Efnb1
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; vision/eye phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; embryo phenotype; respiratory system phenotype; immune system phenotype; skeleton phenotype; hearing/vestibular/ear 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); limbs/digits/tail phenotype; digestive/alimentary phenotype;

Zebrafish Information Network

Gene name
efnb1
Affected structure
hepatoblast
Phenotype tag
abnormal
Phenotype quality
anterior orientation

Gene ontology

Biological process
neural crest cell migration;cell adhesion;cell-cell signaling;axon guidance;embryonic pattern specification;peptidyl-tyrosine phosphorylation;T cell costimulation;positive regulation of T cell proliferation;ephrin receptor signaling pathway
Cellular component
nucleus;cytoplasm;plasma membrane;integral component of plasma membrane;membrane raft;synapse;extracellular exosome
Molecular function
protein tyrosine kinase activity;protein binding;ephrin receptor binding