HPGDS
hematopoietic prostaglandin D synthase, the group of Soluble glutathione S-transferases
Basic information
Region (hg38): 4:94298535-94342876
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 HPGDS 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 | 2 | |||||
| missense | 11 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 5 |
Variants in HPGDS
This is a list of pathogenic ClinVar variants found in the HPGDS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-94299483-G-C | Benign (Jun 08, 2018) | |||
| 4-94299510-C-G | not specified | Uncertain significance (Feb 17, 2024) | ||
| 4-94299521-C-T | Benign (Jun 13, 2018) | |||
| 4-94302198-A-G | Benign (Jun 08, 2018) | |||
| 4-94302225-A-G | not specified | Uncertain significance (Apr 26, 2023) | ||
| 4-94302242-C-G | not specified | Likely benign (Dec 27, 2023) | ||
| 4-94308674-A-G | not specified | Uncertain significance (Jul 19, 2022) | ||
| 4-94308699-T-C | Benign (Jun 08, 2018) | |||
| 4-94308729-T-G | not specified | Uncertain significance (Jan 06, 2023) | ||
| 4-94317914-T-C | not specified | Uncertain significance (Dec 14, 2023) | ||
| 4-94334521-C-T | not specified | Uncertain significance (Nov 29, 2021) | ||
| 4-94334548-G-C | not specified | Uncertain significance (Aug 04, 2023) | ||
| 4-94334588-T-C | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HPGDS | protein_coding | protein_coding | ENST00000295256 | 5 | 44342 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000181 | 0.263 | 125708 | 0 | 31 | 125739 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.03 | 135 | 105 | 1.28 | 0.00000504 | 1313 |
| Missense in Polyphen | 50 | 35.199 | 1.4205 | 448 | ||
| Synonymous | -0.431 | 40 | 36.7 | 1.09 | 0.00000191 | 348 |
| Loss of Function | 0.136 | 9 | 9.45 | 0.952 | 3.97e-7 | 125 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000126 | 0.000125 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000112 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000232 | 0.000229 |
| Middle Eastern | 0.000112 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Bifunctional enzyme which catalyzes both the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation, and the conjugation of glutathione with a wide range of aryl halides and organic isothiocyanates. Also exhibits low glutathione-peroxidase activity towards cumene hydroperoxide. {ECO:0000269|PubMed:10824118, ECO:0000269|PubMed:11672424, ECO:0000269|PubMed:12627223, ECO:0000269|PubMed:15113825, ECO:0000269|PubMed:16547010, ECO:0000269|PubMed:19939518, ECO:0000269|PubMed:9353279, ECO:0000269|PubMed:9425264}.;
- Pathway
- Glutathione metabolism - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Aryl Hydrocarbon Receptor;Prostaglandin Synthesis and Regulation;eicosanoid metabolism;Glutathione conjugation;Metabolism of lipids;Phase II - Conjugation of compounds;Synthesis of Prostaglandins (PG) and Thromboxanes (TX);Prostaglandin Leukotriene metabolism;Arachidonic acid metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;C20 prostanoid biosynthesis
(Consensus)
Intolerance Scores
- loftool
- 0.841
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 67.03
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.284
- ghis
- 0.488
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.975
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hpgds
- Phenotype
- 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; 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); 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); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- prostaglandin metabolic process;signal transduction;locomotory behavior;cyclooxygenase pathway;glutathione derivative biosynthetic process;negative regulation of male germ cell proliferation
- Cellular component
- cytoplasm;cytosol
- Molecular function
- magnesium ion binding;glutathione transferase activity;prostaglandin-D synthase activity;calcium ion binding;protein binding;protein homodimerization activity