PREX1
phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1, the group of Dbl family Rho GEFs|PDZ domain containing|Pleckstrin homology domain containing
Basic information
Region (hg38): 20:48624252-48827999
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (171 variants)
- not_provided (12 variants)
- PREX1-related_disorder (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PREX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020820.4. 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 | 12 | |||||
| missense | 165 | 10 | 175 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 165 | 17 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PREX1 | protein_coding | protein_coding | ENST00000371941 | 40 | 203631 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 3.56e-12 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.69 | 669 | 997 | 0.671 | 0.0000632 | 10897 |
| Missense in Polyphen | 162 | 342.73 | 0.47268 | 3652 | ||
| Synonymous | 1.19 | 390 | 421 | 0.926 | 0.0000285 | 3184 |
| Loss of Function | 8.26 | 3 | 85.3 | 0.0352 | 0.00000407 | 1006 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000968 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000925 | 0.0000924 |
| 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: Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Chemokine signaling pathway;Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Regulation of RAC1 activity;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.0897
- rvis_EVS
- 0.07
- rvis_percentile_EVS
- 58.96
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.485
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.888
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | Medium |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Prex1
- Phenotype
- growth/size/body region phenotype; cellular phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; hematopoietic system 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);
Zebrafish Information Network
- Gene name
- prex1
- Affected structure
- GTPase activity
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- superoxide metabolic process;G protein-coupled receptor signaling pathway;actin filament polymerization;T cell differentiation;positive regulation of cell migration;neutrophil chemotaxis;regulation of actin filament polymerization;regulation of Rho protein signal transduction;intracellular signal transduction;neutrophil activation;positive regulation of apoptotic process;positive regulation of GTPase activity;regulation of dendrite development;regulation of small GTPase mediated signal transduction;positive regulation of substrate adhesion-dependent cell spreading
- Cellular component
- cytosol;plasma membrane;growth cone;dendritic shaft;perinuclear region of cytoplasm
- Molecular function
- guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding;phospholipid binding;enzyme binding;Rac guanyl-nucleotide exchange factor activity