HPGDS (hematopoietic prostaglandin D synthase) - Rat Genome Database

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Gene: HPGDS (hematopoietic prostaglandin D synthase) Homo sapiens
Analyze
Symbol: HPGDS
Name: hematopoietic prostaglandin D synthase
RGD ID: 732845
HGNC Page HGNC
Description: Enables metal ion binding activity; prostaglandin-D synthase activity; and protein homodimerization activity. Involved in prostaglandin metabolic process. Located in cytosol and nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: glutathione S-transferase sigma; glutathione-dependent PGD synthase; glutathione-dependent PGD synthetase; glutathione-requiring prostaglandin D synthase; GST class-sigma; GSTS; GSTS1; GSTS1-1; hematopoietic prostaglandin D2 synthase; PGD2; PGDS; prostaglandin-H2 D-isomerase
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl494,298,535 - 94,342,876 (-)EnsemblGRCh38hg38GRCh38
GRCh38494,298,535 - 94,342,876 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37495,219,686 - 95,263,987 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36495,438,730 - 95,483,050 (-)NCBINCBI36hg18NCBI36
Build 34495,577,633 - 95,612,968NCBI
Celera492,516,831 - 92,561,280 (-)NCBI
Cytogenetic Map4q22.3NCBI
HuRef490,957,458 - 91,001,835 (-)NCBIHuRef
CHM1_1495,196,420 - 95,241,397 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9353279   PMID:9425264   PMID:9475419   PMID:10781097   PMID:10824118   PMID:10998423   PMID:11068878   PMID:11672424   PMID:12002745   PMID:12477932   PMID:12627223   PMID:12707014  
PMID:12895599   PMID:15113825   PMID:15489334   PMID:18029348   PMID:18341273   PMID:18946232   PMID:19124506   PMID:19181746   PMID:19247692   PMID:19276290   PMID:19913121   PMID:20074808  
PMID:20628086   PMID:21683347   PMID:21821144   PMID:21873635   PMID:22049022   PMID:22418579   PMID:23666239   PMID:24996417   PMID:25416956   PMID:27145233   PMID:27485270   PMID:30021884  
PMID:31515488   PMID:32296183  


Genomics

Comparative Map Data
HPGDS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl494,298,535 - 94,342,876 (-)EnsemblGRCh38hg38GRCh38
GRCh38494,298,535 - 94,342,876 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37495,219,686 - 95,263,987 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36495,438,730 - 95,483,050 (-)NCBINCBI36hg18NCBI36
Build 34495,577,633 - 95,612,968NCBI
Celera492,516,831 - 92,561,280 (-)NCBI
Cytogenetic Map4q22.3NCBI
HuRef490,957,458 - 91,001,835 (-)NCBIHuRef
CHM1_1495,196,420 - 95,241,397 (-)NCBICHM1_1
Hpgds
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39665,094,277 - 65,121,961 (-)NCBIGRCm39mm39
GRCm39 Ensembl665,094,277 - 65,121,892 (-)Ensembl
GRCm38665,117,293 - 65,144,981 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl665,117,293 - 65,144,908 (-)EnsemblGRCm38mm10GRCm38
MGSCv37665,067,287 - 65,094,724 (-)NCBIGRCm37mm9NCBIm37
MGSCv36665,048,942 - 65,074,308 (-)NCBImm8
Celera667,246,090 - 67,273,526 (-)NCBICelera
Cytogenetic Map6C1NCBI
Hpgds
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2494,368,426 - 94,397,931 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl494,373,342 - 94,397,883 (-)Ensembl
Rnor_6.0495,945,356 - 95,970,666 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl495,946,025 - 95,970,666 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04160,734,255 - 160,758,902 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4494,611,607 - 94,636,147 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1494,856,088 - 94,880,628 (-)NCBI
Celera489,106,678 - 89,131,218 (-)NCBICelera
Cytogenetic Map4q31NCBI
HPGDS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1497,332,231 - 97,375,684 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl497,332,231 - 97,375,815 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0486,659,551 - 86,702,995 (-)NCBIMhudiblu_PPA_v0panPan3
HPGDS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13217,172,372 - 17,196,851 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3217,121,968 - 17,196,851 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3224,752,940 - 24,777,413 (+)NCBI
ROS_Cfam_1.03217,315,689 - 17,375,451 (-)NCBI
UMICH_Zoey_3.13217,323,037 - 17,347,505 (-)NCBI
UNSW_CanFamBas_1.03217,137,331 - 17,161,789 (-)NCBI
UU_Cfam_GSD_1.03222,730,052 - 22,754,426 (+)NCBI
Hpgds
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530124,462,666 - 24,540,537 (+)NCBI
SpeTri2.0NW_0049366871,806,452 - 1,884,310 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HPGDS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8125,382,952 - 125,405,955 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18125,375,906 - 125,406,066 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28134,662,192 - 134,692,377 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HPGDS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1742,555,151 - 42,592,457 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl742,553,848 - 42,592,400 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603720,918,448 - 20,961,381 (-)NCBIVero_WHO_p1.0
Hpgds
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475722,114,917 - 22,166,833 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
PGDS_9545  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37495,220,262 - 95,220,794UniSTSGRCh37
Build 36495,439,285 - 95,439,817RGDNCBI36
Celera492,517,386 - 92,517,918RGD
HuRef490,958,013 - 90,958,545UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:538
Count of miRNA genes:440
Interacting mature miRNAs:475
Transcripts:ENST00000295256, ENST00000506331, ENST00000514774
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 100 21 8 7 36 6 169 66 29 11 53 167 2 186 36 2
Low 2147 1667 896 342 456 189 3212 1128 2351 281 1006 897 156 1 1005 2048 2 1
Below cutoff 78 1154 749 241 915 233 761 930 1220 81 303 322 8 13 686 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000295256   ⟹   ENSP00000295256
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl494,298,535 - 94,342,836 (-)Ensembl
RefSeq Acc Id: ENST00000506331
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl494,334,181 - 94,342,876 (-)Ensembl
RefSeq Acc Id: ENST00000514774
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl494,303,763 - 94,342,865 (-)Ensembl
RefSeq Acc Id: NM_014485   ⟹   NP_055300
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38494,298,535 - 94,342,836 (-)NCBI
GRCh37495,219,707 - 95,264,027 (-)ENTREZGENE
GRCh37495,219,707 - 95,264,027 (-)NCBI
Build 36495,438,730 - 95,483,050 (-)NCBI Archive
HuRef490,957,458 - 91,001,835 (-)ENTREZGENE
CHM1_1495,196,420 - 95,241,397 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005262932   ⟹   XP_005262989
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38494,299,304 - 94,342,876 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_055300   ⟸   NM_014485
- UniProtKB: O60760 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_005262989   ⟸   XM_005262932
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000295256   ⟸   ENST00000295256
Protein Domains
GST C-terminal   GST N-terminal

Promoters
RGD ID:6868054
Promoter ID:EPDNEW_H7192
Type:initiation region
Name:HPGDS_1
Description:hematopoietic prostaglandin D synthase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38494,342,836 - 94,342,896EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q22.2-32.3(chr4:92913386-165299707)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|See cases [RCV000051775] Chr4:92913386..165299707 [GRCh38]
Chr4:93834537..166220859 [GRCh37]
Chr4:94053560..166440309 [NCBI36]
Chr4:4q22.2-32.3
pathogenic
GRCh38/hg38 4q12-22.3(chr4:51831622-97505618)x3 copy number gain See cases [RCV000051772] Chr4:51831622..97505618 [GRCh38]
Chr4:52697788..98426769 [GRCh37]
Chr4:52392545..98645792 [NCBI36]
Chr4:4q12-22.3
pathogenic
NM_014485.2(HPGDS):c.154C>T (p.Pro52Ser) single nucleotide variant Malignant melanoma [RCV000066584] Chr4:94317945 [GRCh38]
Chr4:95239096 [GRCh37]
Chr4:95458119 [NCBI36]
Chr4:4q22.3
not provided
GRCh38/hg38 4q21.21-22.3(chr4:80879777-94809447)x1 copy number loss See cases [RCV000134977] Chr4:80879777..94809447 [GRCh38]
Chr4:81800931..95730598 [GRCh37]
Chr4:82019955..95949621 [NCBI36]
Chr4:4q21.21-22.3
pathogenic
GRCh38/hg38 4q21.21-24(chr4:80427023-100855441)x1 copy number loss See cases [RCV000137269] Chr4:80427023..100855441 [GRCh38]
Chr4:81348177..101776598 [GRCh37]
Chr4:81567201..101995621 [NCBI36]
Chr4:4q21.21-24
pathogenic
GRCh38/hg38 4q22.1-22.3(chr4:92087558-94308725)x1 copy number loss See cases [RCV000137734] Chr4:92087558..94308725 [GRCh38]
Chr4:93008709..95229876 [GRCh37]
Chr4:93227732..95448899 [NCBI36]
Chr4:4q22.1-22.3
uncertain significance
GRCh38/hg38 4q22.1-24(chr4:92610413-101521991)x1 copy number loss See cases [RCV000140412] Chr4:92610413..101521991 [GRCh38]
Chr4:93531564..102443148 [GRCh37]
Chr4:93750587..102662171 [NCBI36]
Chr4:4q22.1-24
pathogenic
GRCh38/hg38 4q22.2-22.3(chr4:94071164-94561427)x4 copy number gain See cases [RCV000141390] Chr4:94071164..94561427 [GRCh38]
Chr4:94992315..95482578 [GRCh37]
Chr4:95211338..95701601 [NCBI36]
Chr4:4q22.2-22.3
uncertain significance
GRCh38/hg38 4q13.2-22.3(chr4:68686088-95294456)x3 copy number gain See cases [RCV000143458] Chr4:68686088..95294456 [GRCh38]
Chr4:69551806..96215607 [GRCh37]
Chr4:69234401..96434630 [NCBI36]
Chr4:4q13.2-22.3
pathogenic
GRCh37/hg19 4q22.3(chr4:95263892-95492115)x3 copy number gain See cases [RCV000446447] Chr4:95263892..95492115 [GRCh37]
Chr4:4q22.3
likely benign
GRCh37/hg19 4p16.3-q35.2(chr4:12440-190904441)x3 copy number gain See cases [RCV000446653] Chr4:12440..190904441 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4q21.23-24(chr4:85805268-103678797)x1 copy number loss See cases [RCV000445741] Chr4:85805268..103678797 [GRCh37]
Chr4:4q21.23-24
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473) copy number gain See cases [RCV000510453] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4q22.1-35.2(chr4:93071152-190957473)x3 copy number gain See cases [RCV000510970] Chr4:93071152..190957473 [GRCh37]
Chr4:4q22.1-35.2
pathogenic
GRCh37/hg19 4q22.1-24(chr4:92201567-103043808)x1 copy number loss See cases [RCV000511194] Chr4:92201567..103043808 [GRCh37]
Chr4:4q22.1-24
pathogenic
GRCh37/hg19 4q22.1-22.3(chr4:89891197-98235479)x1 copy number loss See cases [RCV000510980] Chr4:89891197..98235479 [GRCh37]
Chr4:4q22.1-22.3
likely pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473)x3 copy number gain See cases [RCV000512241] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4q22.1-22.3(chr4:90005204-96971785)x1 copy number loss not provided [RCV000682434] Chr4:90005204..96971785 [GRCh37]
Chr4:4q22.1-22.3
pathogenic
GRCh37/hg19 4q21.21-22.3(chr4:81314915-96636651)x1 copy number loss not provided [RCV000682426] Chr4:81314915..96636651 [GRCh37]
Chr4:4q21.21-22.3
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190915650)x3 copy number gain not provided [RCV000743155] Chr4:49450..190915650 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4q22.1-22.3(chr4:93344512-95415483)x3 copy number gain not provided [RCV000743825] Chr4:93344512..95415483 [GRCh37]
Chr4:4q22.1-22.3
uncertain significance
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190963766)x3 copy number gain not provided [RCV000743156] Chr4:49450..190963766 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:11525-191028879)x3 copy number gain not provided [RCV000743147] Chr4:11525..191028879 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
NM_014485.3(HPGDS):c.42A>G (p.Arg14=) single nucleotide variant not provided [RCV000950669] Chr4:94334588 [GRCh38]
Chr4:95255739 [GRCh37]
Chr4:4q22.3
benign
NM_014485.3(HPGDS):c.597C>G (p.Leu199=) single nucleotide variant not provided [RCV000973177] Chr4:94299483 [GRCh38]
Chr4:95220634 [GRCh37]
Chr4:4q22.3
benign
NM_014485.3(HPGDS):c.559G>A (p.Val187Ile) single nucleotide variant not provided [RCV000973178] Chr4:94299521 [GRCh38]
Chr4:95220672 [GRCh37]
Chr4:4q22.3
benign
NM_014485.3(HPGDS):c.383T>C (p.Met128Thr) single nucleotide variant not provided [RCV000973179] Chr4:94302198 [GRCh38]
Chr4:95223349 [GRCh37]
Chr4:4q22.3
benign
NM_014485.3(HPGDS):c.271A>G (p.Ile91Val) single nucleotide variant not provided [RCV000973180] Chr4:94308699 [GRCh38]
Chr4:95229850 [GRCh37]
Chr4:4q22.3
benign
GRCh37/hg19 4q22.3(chr4:95240876-95497772)x3 copy number gain not provided [RCV001005576] Chr4:95240876..95497772 [GRCh37]
Chr4:4q22.3
uncertain significance
GRCh37/hg19 4q22.2-24(chr4:94692345-101308220)x1 copy number loss not provided [RCV001259285] Chr4:94692345..101308220 [GRCh37]
Chr4:4q22.2-24
likely pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17890 AgrOrtholog
COSMIC HPGDS COSMIC
Ensembl Genes ENSG00000163106 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000295256 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000295256 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000163106 GTEx
HGNC ID HGNC:17890 ENTREZGENE
Human Proteome Map HPGDS Human Proteome Map
InterPro Glutathione-S-Trfase_C-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione-S-Trfase_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione_S-Trfase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GST_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:27306 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 27306 ENTREZGENE
OMIM 602598 OMIM
Pfam GST_C_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GST_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA165664133 PharmGKB
PROSITE GST_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GST_NTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52833 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A384P5J0_HUMAN UniProtKB/TrEMBL
  HPGDS_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6FHT9 UniProtKB/Swiss-Prot