PEBP1
Basic information
Region (hg38): 12:118136124-118145584
Previous symbols: [ "PBP" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (8 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002567.4. 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 | 0 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PEBP1 | protein_coding | protein_coding | ENST00000261313 | 4 | 9727 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0917 | 0.873 | 125713 | 0 | 35 | 125748 | 0.000139 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.942 | 83 | 111 | 0.748 | 0.00000638 | 1202 |
| Missense in Polyphen | 20 | 26.198 | 0.76341 | 278 | ||
| Synonymous | -0.127 | 53 | 51.8 | 1.02 | 0.00000348 | 371 |
| Loss of Function | 1.80 | 3 | 8.75 | 0.343 | 4.57e-7 | 94 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000125 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000266 | 0.000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000167 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Binds ATP, opioids and phosphatidylethanolamine. Has lower affinity for phosphatidylinositol and phosphatidylcholine. Serine protease inhibitor which inhibits thrombin, neuropsin and chymotrypsin but not trypsin, tissue type plasminogen activator and elastase (By similarity). Inhibits the kinase activity of RAF1 by inhibiting its activation and by dissociating the RAF1/MEK complex and acting as a competitive inhibitor of MEK phosphorylation. {ECO:0000250, ECO:0000269|PubMed:18294816}.;
- Pathway
- EGF-Ncore;EGF-EGFR Signaling Pathway;MAP2K and MAPK activation;Disease;Signal Transduction;signal transduction through il1r;EGFR1;ErbB1 downstream signaling;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Signaling by RAS mutants;Signaling by high-kinase activity BRAF mutants;Signaling by moderate kinase activity BRAF mutants;Paradoxical activation of RAF signaling by kinase inactive BRAF;Aurora B signaling;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction
(Consensus)
Recessive Scores
- pRec
- 0.284
Intolerance Scores
- loftool
- 0.554
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 73.97
Haploinsufficiency Scores
- pHI
- 0.0688
- hipred
- Y
- hipred_score
- 0.835
- ghis
- 0.413
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pebp1
- Phenotype
- taste/olfaction phenotype;
Gene ontology
- Biological process
- MAPK cascade;regulation of neurotransmitter levels;regulation of the force of heart contraction;response to oxidative stress;aging;response to heat;response to wounding;response to toxic substance;response to organonitrogen compound;negative regulation of endopeptidase activity;response to activity;hippocampus development;negative regulation of MAPK cascade;positive regulation of cAMP-mediated signaling;response to ethanol;positive regulation of mitotic nuclear division;sperm capacitation;response to corticosterone;response to cAMP;response to calcium ion;positive regulation of acetylcholine metabolic process
- Cellular component
- extracellular space;nucleus;mitochondrion;mitochondrial outer membrane;Golgi apparatus;cytosol;synaptic vesicle;cell surface;neuronal cell body;myelin sheath;axon terminus;apical part of cell;extracellular exosome
- Molecular function
- RNA binding;serine-type endopeptidase inhibitor activity;signaling receptor binding;protein binding;ATP binding;phosphatidylethanolamine binding;enzyme binding;protein kinase binding;mitogen-activated protein kinase binding