EFNB1
Basic information
Region (hg38): X:68829021-68842160
Previous symbols: [ "EPLG2", "CFNS" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Craniofrontonasal dysplasia | XL | General | 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 | Craniofacial; Musculoskeletal | 15166289; 15124102; 15959873; 16639408; 17941886; 18627045; 20734337; 21385071; 23509643 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 18 | 21 | ||||
missense | 11 | 17 | 70 | 104 | ||
nonsense | 13 | 16 | ||||
start loss | 1 | 1 | ||||
frameshift | 13 | 21 | ||||
splice donor/acceptor (+/-2bp) | 7 | |||||
Total | 42 | 30 | 72 | 22 | 4 |
Highest pathogenic variant AF is 9.1527403e-7
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EFNB1 | protein_coding | protein_coding | ENST00000204961 | 5 | 13151 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.933 | 0.0672 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.59 | 100 | 156 | 0.641 | 0.0000132 | 2241 |
Missense in Polyphen | 31 | 64.037 | 0.4841 | 934 | ||
Synonymous | 0.263 | 65 | 67.8 | 0.959 | 0.00000584 | 712 |
Loss of Function | 2.71 | 0 | 8.58 | 0.00 | 6.16e-7 | 148 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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