PHLDA3
Basic information
Region (hg38): 1:201464278-201469237
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 PHLDA3 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 | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in PHLDA3
This is a list of pathogenic ClinVar variants found in the PHLDA3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-201468426-C-T | not specified | Uncertain significance (Dec 19, 2023) | ||
| 1-201468474-A-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 1-201468496-C-A | not specified | Uncertain significance (Oct 14, 2023) | ||
| 1-201468618-G-T | not specified | Uncertain significance (Mar 18, 2024) | ||
| 1-201468622-G-T | not specified | Uncertain significance (Dec 03, 2024) | ||
| 1-201468699-G-C | not specified | Uncertain significance (Jul 10, 2024) | ||
| 1-201468749-C-T | not specified | Uncertain significance (May 13, 2024) | ||
| 1-201468773-G-A | not specified | Uncertain significance (May 26, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PHLDA3 | protein_coding | protein_coding | ENST00000367311 | 1 | 3746 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.250 | 0.651 | 125658 | 0 | 31 | 125689 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.150 | 75 | 78.8 | 0.952 | 0.00000370 | 802 |
| Missense in Polyphen | 26 | 23.962 | 1.0851 | 268 | ||
| Synonymous | -2.03 | 55 | 38.9 | 1.41 | 0.00000182 | 287 |
| Loss of Function | 1.21 | 1 | 3.41 | 0.294 | 1.46e-7 | 35 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00141 | 0.00142 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000274 | 0.0000264 |
| Middle Eastern | 0.00141 | 0.00142 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: p53/TP53-regulated repressor of Akt/AKT1 signaling. Represses AKT1 by preventing AKT1-binding to membrane lipids, thereby inhibiting AKT1 translocation to the cellular membrane and activation. Contributes to p53/TP53-dependent apoptosis by repressing AKT1 activity. Its direct transcription regulation by p53/TP53 may explain how p53/TP53 can negatively regulate AKT1. May act as a tumor suppressor. {ECO:0000269|PubMed:19203586}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.114
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.33
Haploinsufficiency Scores
- pHI
- 0.0938
- hipred
- N
- hipred_score
- 0.354
- ghis
- 0.498
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Phlda3
- Phenotype
- embryo phenotype;
Gene ontology
- Biological process
- anatomical structure morphogenesis;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation of apoptotic process;negative regulation of protein kinase B signaling
- Cellular component
- cytoplasm;plasma membrane
- Molecular function
- phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-3,4,5-trisphosphate binding;phosphatidylinositol-5-phosphate binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidylinositol-3,5-bisphosphate binding