PTGDR

prostaglandin D2 receptor, the group of Prostaglandin receptors

Basic information

Region (hg38): 14:52267698-52276724

Links

ENSG00000168229 ∙ NCBI:5729 ∙ OMIM:604687 ∙ HGNC:9591 ∙ Uniprot:Q13258 ∙ 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 PTGDR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTGDR 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						0
missense			19	4	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	4	1

Variants in PTGDR

This is a list of pathogenic ClinVar variants found in the PTGDR region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-52267825-C-T		not specified	Uncertain significance (Jul 30, 2024)
14-52267831-A-T		not specified	Uncertain significance (Nov 22, 2023)
14-52267833-C-T			Benign (Aug 03, 2017)
14-52267846-C-T		not specified	Uncertain significance (Dec 13, 2022)
14-52267921-T-C		not specified	Uncertain significance (May 15, 2024)
14-52267968-C-T		not specified	Uncertain significance (May 24, 2023)
14-52267990-C-T		not specified	Uncertain significance (Aug 04, 2024)
14-52268001-A-G		not specified	Likely benign (Jul 06, 2021)
14-52268097-G-A		not specified	Uncertain significance (Jan 04, 2024)
14-52268104-C-T		not specified	Likely benign (Nov 05, 2021)
14-52268109-G-T		not specified	Uncertain significance (Nov 14, 2024)
14-52268298-G-A		not specified	Uncertain significance (Feb 15, 2023)
14-52268328-G-A		not specified	Uncertain significance (Jun 06, 2023)
14-52268385-G-A		not specified	Uncertain significance (Sep 26, 2023)
14-52268398-C-T		not specified	Uncertain significance (Sep 26, 2024)
14-52268410-A-T		not specified	Uncertain significance (Sep 20, 2023)
14-52268424-T-C		not specified	Uncertain significance (May 28, 2024)
14-52268524-G-A		not specified	Uncertain significance (May 31, 2023)
14-52268535-A-G		not specified	Uncertain significance (Dec 05, 2024)
14-52268554-G-A		not specified	Uncertain significance (Oct 06, 2021)
14-52268557-C-T		not specified	Uncertain significance (Nov 25, 2024)
14-52268572-C-G			Likely benign (Jun 01, 2024)
14-52268610-C-A		not specified	Uncertain significance (Mar 27, 2023)
14-52268617-C-A		not specified	Uncertain significance (Mar 18, 2024)
14-52268622-A-G		not specified	Uncertain significance (May 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTGDR	protein_coding	protein_coding	ENST00000306051	2	9012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000358	0.369	125049	7	692	125748	0.00278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.940	238	201	1.19	0.00000964	2273
Missense in Polyphen		90	80.23	1.1218		983
Synonymous	-0.618	101	93.4	1.08	0.00000453	814
Loss of Function	0.395	9	10.4	0.868	6.20e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0395	0.0394
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for prostaglandin D2 (PGD2). The activity of this receptor is mainly mediated by G(s) proteins that stimulate adenylate cyclase, resulting in an elevation of intracellular cAMP. A mobilization of calcium is also observed, but without formation of inositol 1,4,5-trisphosphate (By similarity). {ECO:0000250}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;Intracellular Signalling Through PGD2 receptor and Prostaglandin D2;Small Ligand GPCRs;GPCRs, Class A Rhodopsin-like;Prostaglandin Synthesis and Regulation;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Prostanoid ligand receptors;Eicosanoid ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Thromboxane A2 receptor signaling;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.239

Intolerance Scores

• loftool: 0.742
• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.52

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0450

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ptgdr
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; muscle 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); 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

Gene ontology

• Biological process: inflammatory response;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;male sex determination;sleep;adenosine metabolic process;cellular response to prostaglandin D stimulus
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: prostaglandin J receptor activity;prostaglandin D receptor activity;protein binding