PROK1
Basic information
Region (hg38): 1:110451149-110457358
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 PROK1 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 | 1 | |||||
| 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 | 1 |
Variants in PROK1
This is a list of pathogenic ClinVar variants found in the PROK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-110451235-G-A | not specified | Uncertain significance (Oct 16, 2024) | ||
| 1-110453962-C-A | not specified | Uncertain significance (Feb 03, 2022) | ||
| 1-110453971-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 1-110454003-G-T | not specified | Uncertain significance (Jun 11, 2021) | ||
| 1-110454034-T-C | not specified | Uncertain significance (Aug 01, 2024) | ||
| 1-110454050-G-T | Benign (Nov 03, 2017) | |||
| 1-110454067-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 1-110456259-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
| 1-110456293-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 1-110456296-G-A | not specified | Uncertain significance (Jan 23, 2023) | ||
| 1-110456317-G-A | not specified | Uncertain significance (Apr 01, 2024) | ||
| 1-110456341-T-A | not specified | Uncertain significance (Mar 07, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PROK1 | protein_coding | protein_coding | ENST00000271331 | 3 | 6155 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000617 | 0.154 | 125713 | 0 | 35 | 125748 | 0.000139 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.186 | 71 | 66.7 | 1.06 | 0.00000436 | 672 |
| Missense in Polyphen | 25 | 27.271 | 0.91673 | 274 | ||
| Synonymous | 0.530 | 24 | 27.5 | 0.872 | 0.00000174 | 213 |
| Loss of Function | -0.667 | 7 | 5.34 | 1.31 | 3.79e-7 | 49 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000506 | 0.000506 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.000114 | 0.000114 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000653 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Potently contracts gastrointestinal (GI) smooth muscle. Induces proliferation, migration and fenestration (the formation of membrane discontinuities) in capillary endothelial cells derived from endocrine glands. Has little or no effect on a variety of other endothelial and non-endothelial cell types. Induces proliferation and differentiation, but not migration, of enteric neural crest cells. Directly influences neuroblastoma progression by promoting the proliferation and migration of neuroblastoma cells. Positively regulates PTGS2 expression and prostaglandin synthesis. May play a role in placentation. May play a role in normal and pathological testis angiogenesis. {ECO:0000269|PubMed:11259612, ECO:0000269|PubMed:11528470, ECO:0000269|PubMed:15292351, ECO:0000269|PubMed:17289879, ECO:0000269|PubMed:18339712}.;
- Pathway
- Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (q) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- loftool
- 0.496
- rvis_EVS
- 0.53
- rvis_percentile_EVS
- 80.58
Haploinsufficiency Scores
- pHI
- 0.195
- hipred
- N
- hipred_score
- 0.278
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prok1
- Phenotype
Gene ontology
- Biological process
- activation of MAPK activity;angiogenesis;G protein-coupled receptor signaling pathway;circadian rhythm;positive regulation of cell population proliferation;regulation of signaling receptor activity;regulation of angiogenesis;positive regulation of cell division
- Cellular component
- extracellular region
- Molecular function
- G protein-coupled receptor binding;growth factor activity