PLXNB3
Basic information
Region (hg38): X:153764196-153779346
Previous symbols: [ "PLXN6" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (278 variants)
- not_provided (62 variants)
- PLXNB3-related_disorder (11 variants)
- Neurodevelopmental_disorder (1 variants)
- Autism_spectrum_disorder (1 variants)
- PLXNB3-related_Intellectual_disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXNB3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005393.3. 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 | 13 | 11 | 25 | |||
| missense | 256 | 45 | 307 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 259 | 59 | 17 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLXNB3 | protein_coding | protein_coding | ENST00000538966 | 35 | 15151 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.232 | 0.768 | 125586 | 14 | 16 | 125616 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.227 | 805 | 823 | 0.978 | 0.0000752 | 12294 |
| Missense in Polyphen | 197 | 296.35 | 0.66474 | 4869 | ||
| Synonymous | -4.49 | 496 | 384 | 1.29 | 0.0000375 | 4166 |
| Loss of Function | 5.30 | 13 | 55.7 | 0.234 | 0.00000385 | 921 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000116 | 0.0000988 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000340 | 0.000231 |
| European (Non-Finnish) | 0.000206 | 0.000141 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000411 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration. Stimulates neurite outgrowth and mediates Ca(2+)/Mg(2+)-dependent cell aggregation. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. {ECO:0000269|PubMed:15218527, ECO:0000269|PubMed:20696765, ECO:0000269|PubMed:21706053}.;
- Pathway
- Axon guidance - Homo sapiens (human);Developmental Biology;Other semaphorin interactions;Semaphorin interactions;Axon guidance
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.441
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.72
Haploinsufficiency Scores
- pHI
- 0.183
- hipred
- N
- hipred_score
- 0.471
- ghis
- 0.527
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.878
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Plxnb3
- 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);
Gene ontology
- Biological process
- positive regulation of endothelial cell proliferation;homophilic cell adhesion via plasma membrane adhesion molecules;negative regulation of cell adhesion;regulation of cell shape;negative regulation of lamellipodium assembly;positive regulation of neuron projection development;regulation of cell migration;negative regulation of cell migration;negative regulation of GTPase activity;regulation of GTPase activity;positive regulation of axonogenesis;positive chemotaxis;cell chemotaxis;semaphorin-plexin signaling pathway;semaphorin-plexin signaling pathway involved in axon guidance
- Cellular component
- semaphorin receptor complex;plasma membrane;integral component of plasma membrane;cell surface
- Molecular function
- protein binding;semaphorin receptor activity;protein domain specific binding;Rho GDP-dissociation inhibitor binding;cell-cell adhesion mediator activity