PAEP
Basic information
Region (hg38): 9:135561756-135566955
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Kleefstra syndrome 1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAEP 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 | 4 | |||||
| missense | 15 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 5 | 3 |
Variants in PAEP
This is a list of pathogenic ClinVar variants found in the PAEP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PAEP | protein_coding | protein_coding | ENST00000479141 | 6 | 5200 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.11e-8 | 0.0967 | 125728 | 0 | 16 | 125744 | 0.0000636 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.518 | 85 | 99.5 | 0.854 | 0.00000508 | 1166 |
| Missense in Polyphen | 28 | 29.11 | 0.96187 | 376 | ||
| Synonymous | -1.42 | 57 | 44.9 | 1.27 | 0.00000290 | 335 |
| Loss of Function | -0.269 | 11 | 10.1 | 1.09 | 4.28e-7 | 119 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000236 | 0.000235 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000442 | 0.0000439 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Glycoprotein that regulates critical steps during fertilization and also has immunomonomodulatory effects. Four glycoforms, namely glycodelin-S, -A, -F and -C have been identified in reproductive tissues that differ in glycosylation and biological activity. Glycodelin-A has contraceptive and immunosuppressive activities (PubMed:9918684, PubMed:7531163). Glycodelin-C stimulates binding of spermatozoa to the zona pellucida (PubMed:17192260). Glycodelin-F inhibits spermatozoa- zona pellucida binding and significantly suppresses progesterone- induced acrosome reaction of spermatozoa (PubMed:12672671). Glycodelin-S in seminal plasma maintains the uncapacitated state of human spermatozoa (PubMed:15883155). {ECO:0000269|PubMed:12672671, ECO:0000269|PubMed:15883155, ECO:0000269|PubMed:17192260, ECO:0000269|PubMed:7531163, ECO:0000269|PubMed:9918684}.;
Recessive Scores
- pRec
- 0.204
Intolerance Scores
- loftool
- 0.782
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.18
Haploinsufficiency Scores
- pHI
- 0.0829
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.702
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- apoptotic process;multicellular organism development;positive regulation of granulocyte macrophage colony-stimulating factor production;negative regulation of sperm capacitation;regulation of binding of sperm to zona pellucida;positive regulation of interleukin-13 secretion;positive regulation of interleukin-6 secretion
- Cellular component
- extracellular region
- Molecular function
- protein binding;small molecule binding