PTGDS
prostaglandin D2 synthase, the group of Lipocalins
Basic information
Region (hg38): 9:136975092-136981742
Links
Phenotypes
GenCC
Source:
No genCC data.
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 PTGDS 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 5 | 1 | 2 |
Variants in PTGDS
This is a list of pathogenic ClinVar variants found in the PTGDS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-136977636-C-G | not specified | Uncertain significance (Sep 29, 2023) | ||
| 9-136978984-T-C | Benign (Mar 29, 2018) | |||
| 9-136978985-C-T | Benign (Mar 29, 2018) | |||
| 9-136979044-C-T | not specified | Uncertain significance (Nov 27, 2023) | ||
| 9-136979984-G-A | not specified | Likely benign (Jun 07, 2023) | ||
| 9-136979999-G-A | not specified | Uncertain significance (Nov 03, 2023) | ||
| 9-136980066-C-T | Benign (Apr 03, 2018) | |||
| 9-136980188-A-G | not specified | Uncertain significance (Jan 31, 2024) | ||
| 9-136980227-G-A | not specified | Likely benign (May 26, 2024) | ||
| 9-136980271-C-G | not specified | Uncertain significance (Jun 21, 2023) | ||
| 9-136980846-G-A | Benign (Apr 09, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTGDS | protein_coding | protein_coding | ENST00000371625 | 6 | 7932 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00509 | 0.971 | 125661 | 0 | 29 | 125690 | 0.000115 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.531 | 101 | 117 | 0.862 | 0.00000724 | 1218 |
| Missense in Polyphen | 24 | 33.42 | 0.71812 | 371 | ||
| Synonymous | 0.365 | 51 | 54.4 | 0.937 | 0.00000377 | 377 |
| Loss of Function | 1.98 | 6 | 14.0 | 0.430 | 8.68e-7 | 127 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000204 | 0.000204 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000274 | 0.000272 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000913 | 0.0000880 |
| Middle Eastern | 0.000274 | 0.000272 |
| South Asian | 0.000230 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation. Involved in a variety of CNS functions, such as sedation, NREM sleep and PGE2-induced allodynia, and may have an anti-apoptotic role in oligodendrocytes. Binds small non-substrate lipophilic molecules, including biliverdin, bilirubin, retinal, retinoic acid and thyroid hormone, and may act as a scavenger for harmful hydrophopic molecules and as a secretory retinoid and thyroid hormone transporter. Possibly involved in development and maintenance of the blood-brain, blood-retina, blood-aqueous humor and blood-testis barrier. It is likely to play important roles in both maturation and maintenance of the central nervous system and male reproductive system. {ECO:0000269|PubMed:20667974, ECO:0000269|PubMed:9475419}.;
- Pathway
- Arachidonic acid metabolism - Homo sapiens (human);Etodolac Action Pathway;Ketoprofen Action Pathway;Ibuprofen Action Pathway;Rofecoxib Action Pathway;Acetylsalicylic Acid Action Pathway;Diflunisal Action Pathway;Leukotriene C4 Synthesis Deficiency;Acetaminophen Action Pathway;Celecoxib Action Pathway;Sulindac Action Pathway;Diclofenac Action Pathway;Ketorolac Action Pathway;Naproxen Action Pathway;Etoricoxib Action Pathway;Carprofen Action Pathway;Flurbiprofen Action Pathway;Fenoprofen Action Pathway;Antrafenine Action Pathway;Antipyrine Action Pathway;Lumiracoxib Action Pathway;Magnesium salicylate Action Pathway;Trisalicylate-choline Action Pathway;Nepafenac Action Pathway;Phenylbutazone Action Pathway;Lornoxicam Action Pathway;Salsalate Action Pathway;Tenoxicam Action Pathway;Tiaprofenic Acid Action Pathway;Tolmetin Action Pathway;Salicylic Acid Action Pathway;Salicylate-sodium Action Pathway;Oxaprozin Action Pathway;Valdecoxib Action Pathway;Nabumetone Action Pathway;Indomethacin Action Pathway;Meloxicam Action Pathway;Suprofen Action Pathway;Bromfenac Action Pathway;Mefenamic Acid Action Pathway;Arachidonic Acid Metabolism;Piroxicam Action Pathway;Eicosanoid Synthesis;Prostaglandin Synthesis and Regulation;Metabolism of lipids;Synthesis of Prostaglandins (PG) and Thromboxanes (TX);Prostaglandin Leukotriene metabolism;Arachidonic acid metabolism;Metabolism;Fatty acid metabolism;C20 prostanoid biosynthesis;Prostaglandin formation from arachidonate
(Consensus)
Recessive Scores
- pRec
- 0.0980
Intolerance Scores
- loftool
- 0.726
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.111
- hipred
- N
- hipred_score
- 0.246
- ghis
- 0.520
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptgds
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm; 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); immune system phenotype;
Gene ontology
- Biological process
- prostaglandin biosynthetic process;cyclooxygenase pathway;regulation of circadian sleep/wake cycle, sleep
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum membrane;rough endoplasmic reticulum;Golgi apparatus;nuclear membrane;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- prostaglandin-D synthase activity;retinoid binding;fatty acid binding;protein binding