HPGDS

hematopoietic prostaglandin D synthase, the group of Soluble glutathione S-transferases

Basic information

Region (hg38): 4:94298535-94342876

Links

ENSG00000163106 ∙ NCBI:27306 ∙ OMIM:602598 ∙ HGNC:17890 ∙ Uniprot:O60760 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HPGDS gene.

• not_specified (16 variants)
• not_provided (5 variants)

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. These statistics are base on transcript: NM_000014485.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			15	1	3	19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	1	5

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• hipred: N
• hipred_score: 0.284
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• 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