PREX2
Basic information
Region (hg38): 8:67952046-68237032
Previous symbols: [ "DEPDC2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PREX2 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 | 12 | 12 | 24 | |||
missense | 63 | 76 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 6 | 6 | ||||
non coding | 5 | |||||
Total | 0 | 1 | 64 | 20 | 21 |
Variants in PREX2
This is a list of pathogenic ClinVar variants found in the PREX2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-67952391-G-C | PREX2-related disorder | Likely benign (Nov 01, 2022) | ||
8-67952410-C-G | not specified | Uncertain significance (Jan 02, 2024) | ||
8-67952411-G-T | not specified | Uncertain significance (Jan 09, 2024) | ||
8-67952490-G-A | PREX2-related disorder | Benign (Mar 06, 2019) | ||
8-67952493-G-A | PREX2-related disorder | Benign (Oct 18, 2019) | ||
8-67952516-C-T | not specified | Uncertain significance (Jun 05, 2023) | ||
8-68015357-C-T | Lip and oral cavity carcinoma | association (Nov 02, 2015) | ||
8-68017871-G-A | PREX2-related disorder | Likely benign (Aug 14, 2019) | ||
8-68017892-A-G | not specified | Uncertain significance (Oct 06, 2021) | ||
8-68019579-G-T | not specified | Uncertain significance (Apr 24, 2024) | ||
8-68019605-C-T | PREX2-related disorder | Likely benign (Jun 27, 2019) | ||
8-68019606-G-A | not specified | Uncertain significance (Jun 22, 2023) | ||
8-68022056-T-A | not provided (-) | |||
8-68022107-C-T | PREX2-related disorder | Likely benign (Dec 06, 2019) | ||
8-68022127-G-A | not specified | Uncertain significance (Mar 17, 2016) | ||
8-68027279-G-A | not specified | Uncertain significance (Apr 30, 2024) | ||
8-68027289-T-C | not specified | Uncertain significance (Sep 21, 2021) | ||
8-68030589-C-T | Benign/Likely benign (Aug 01, 2022) | |||
8-68030641-C-T | not specified | Uncertain significance (Dec 14, 2023) | ||
8-68030666-C-T | PREX2-related disorder | Benign (Mar 29, 2018) | ||
8-68038241-G-A | Neoplasm | - (-) | ||
8-68044537-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
8-68044555-A-G | not specified | Uncertain significance (Jun 06, 2022) | ||
8-68044581-G-A | PREX2-related disorder | Likely benign (Jul 22, 2023) | ||
8-68053107-T-C | PREX2-related disorder | Likely benign (Jun 04, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PREX2 | protein_coding | protein_coding | ENST00000288368 | 40 | 284913 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.33e-16 | 1.00 | 125531 | 1 | 216 | 125748 | 0.000863 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.73 | 719 | 862 | 0.834 | 0.0000454 | 10632 |
Missense in Polyphen | 300 | 376.21 | 0.79742 | 4618 | ||
Synonymous | -0.344 | 307 | 299 | 1.03 | 0.0000157 | 2884 |
Loss of Function | 4.57 | 41 | 87.0 | 0.471 | 0.00000403 | 1134 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00376 | 0.00375 |
Ashkenazi Jewish | 0.0000998 | 0.0000992 |
East Asian | 0.000222 | 0.000217 |
Finnish | 0.00327 | 0.00319 |
European (Non-Finnish) | 0.000365 | 0.000360 |
Middle Eastern | 0.000222 | 0.000217 |
South Asian | 0.000393 | 0.000392 |
Other | 0.00117 | 0.00114 |
dbNSFP
Source:
- Function
- FUNCTION: Functions as a RAC1 guanine nucleotide exchange factor (GEF), activating 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. Mediates the activation of RAC1 in a PI3K-dependent manner. May be an important mediator of Rac signaling, acting directly downstream of both G protein- coupled receptors and phosphoinositide 3-kinase. {ECO:0000269|PubMed:15304342, ECO:0000269|PubMed:15304343, ECO:0000269|PubMed:15897194}.;
- Pathway
- Signal Transduction;Regulation of PTEN stability and activity;Regulation of RAC1 activity;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers
(Consensus)
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- 0.582
- rvis_EVS
- -0.67
- rvis_percentile_EVS
- 15.42
Haploinsufficiency Scores
- pHI
- 0.347
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.517
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.186
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prex2
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);
Gene ontology
- Biological process
- G protein-coupled receptor signaling pathway;adult locomotory behavior;phosphatidylinositol 3-kinase signaling;regulation of Rho protein signal transduction;positive regulation of GTPase activity;dendrite morphogenesis
- Cellular component
- cytosol;plasma membrane
- Molecular function
- GTPase activator activity;Rac guanyl-nucleotide exchange factor activity