EFNB1
Basic information
Region (hg38): X:68829020-68842160
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 (74 variants)
- Craniofrontonasal syndrome (33 variants)
- Inborn genetic diseases (15 variants)
- not specified (2 variants)
- EFNB1-related condition (2 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.
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 | 11 | 13 | ||||
missense | 37 | 55 | ||||
nonsense | 12 | |||||
start loss | 0 | |||||
frameshift | 10 | 16 | ||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
splice region ? | 1 | 2 | 1 | 4 | ||
non coding ? | 7 | |||||
Total | 27 | 17 | 39 | 18 | 8 |
Variants in EFNB1
This is a list of pathogenic ClinVar variants found in the EFNB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-68829082-C-T | Likely benign (Dec 12, 2020) | |||
X-68829392-G-T | Benign (Mar 16, 2019) | |||
X-68829498-C-G | Likely benign (Nov 13, 2019) | |||
X-68829771-G-A | EFNB1-related disorder | Likely benign (Mar 05, 2019) | ||
X-68829783-C-T | Inborn genetic diseases | Uncertain significance (Oct 22, 2021) | ||
X-68829794-G-A | EFNB1-related disorder | Likely benign (Jan 26, 2024) | ||
X-68829800-G-A | Craniofrontonasal syndrome | Likely pathogenic (May 20, 2020) | ||
X-68829811-G-A | EFNB1-related disorder | Likely pathogenic (Jul 19, 2023) | ||
X-68829841-GC-G | Craniofrontonasal syndrome | Likely pathogenic (-) | ||
X-68829848-C-T | Likely benign (Dec 19, 2023) | |||
X-68829859-T-TG | Pathogenic (May 26, 2016) | |||
X-68829868-ACCTGGAGCCCGTAT-A | Craniofrontonasal syndrome | Pathogenic (May 02, 2023) | ||
X-68829868-A-ACCTGGAGCCCGTAT | Pathogenic (Jan 30, 2015) | |||
X-68829876-C-G | Uncertain significance (Aug 26, 2020) | |||
X-68829885-T-G | Craniofrontonasal syndrome | Pathogenic (Jun 01, 2006) | ||
X-68829886-G-A | Craniofrontonasal syndrome | Pathogenic (Jun 01, 2006) | ||
X-68829887-G-A | Craniofrontonasal syndrome | Pathogenic (May 20, 2021) | ||
X-68829905-G-C | Craniofrontonasal syndrome | Likely pathogenic (Jan 03, 2024) | ||
X-68829906-T-A | Craniofrontonasal syndrome | Pathogenic (Oct 28, 2016) | ||
X-68829909-G-A | Craniofrontonasal syndrome | Conflicting classifications of pathogenicity (Apr 30, 2023) | ||
X-68829913-C-T | Likely benign (Apr 24, 2023) | |||
X-68830124-C-G | Benign (Feb 14, 2019) | |||
X-68830139-C-G | Benign (Nov 10, 2018) | |||
X-68838318-C-T | Likely benign (May 19, 2020) | |||
X-68838616-G-T | Pathogenic (Dec 01, 2017) |
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