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This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Mul... See more...
Aliases for PHGDH Gene
Aliases for PHGDH Gene
External Ids for PHGDH Gene
- HGNC: 8923
- Entrez Gene: 26227
- Ensembl: ENSG00000092621
- OMIM: 606879
- UniProtKB: O43175
Previous GeneCards Identifiers for PHGDH Gene
- GC01P120701
- GC01P119092
- GC01P119401
- GC01P119600
- GC01P119966
- GC01P120056
- GC01P120202
- GC01P118112
Summaries for PHGDH Gene
-
This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found, however the full-length nature of most are not known. [provided by RefSeq, Aug 2011]
GeneCards Summary for PHGDH Gene
PHGDH (Phosphoglycerate Dehydrogenase) is a Protein Coding gene. Diseases associated with PHGDH include Phosphoglycerate Dehydrogenase Deficiency and Neu-Laxova Syndrome 1. Among its related pathways are One carbon pool by folate and Viral mRNA Translation. Gene Ontology (GO) annotations related to this gene include electron transfer activity and oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. An important paralog of this gene is CTBP2.
UniProtKB/Swiss-Prot Summary for PHGDH Gene
-
Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
Additional gene information for PHGDH Gene
- HGNC(8923)
- Entrez Gene(26227)
- Ensembl(ENSG00000092621)
- OMIM(606879)
- UniProtKB(O43175)
- Open Targets Platform(ENSG00000092621)
- Monarch Initiative
- Search for PHGDH at DataMed
- Search for PHGDH at HumanCyc
No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHGDH Gene
Genomics for PHGDH Gene
GeneHancer (GH) Regulatory Elements Pubs
Promoters and enhancers for PHGDH Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication |
Request up-to-date GeneHancer data (full dataset)
GeneHancers around PHGDH on the GeneHancer Hub at the UCSC Golden Path
Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHGDH
- Top Transcription factor binding sites by QIAGEN in the PHGDH gene promoter:
-
- c-Myc
- CUTL1
- GR
- GR-alpha
- IRF-1
- Max
- Max1
- NRF-2
- PPAR-alpha
Genomic Locations for PHGDH Gene
Genomic Locations for PHGDH Gene
- chr1:119,648,411-119,744,226
- (GRCh38/hg38)
- Size:
- 95,816 bases
- Orientation:
- Plus strand
- chr1:120,202,421-120,286,849
- (GRCh37/hg19)
- Size:
- 84,429 bases
- Orientation:
- Plus strand
Genomic View for PHGDH Gene
Genes around PHGDH on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 1p12 by HGNC
- 1p12 by Entrez Gene
- 1p12 by Ensembl
PHGDH Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for PHGDH Gene
Proteins for PHGDH Gene
-
Protein details for PHGDH Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- O43175-SERA_HUMAN
- Recommended name:
- D-3-phosphoglycerate dehydrogenase
- Protein Accession:
- O43175
- B2RD08
- Q5SZU3
- Q9BQ01
Protein attributes for PHGDH Gene
- Size:
- 533 amino acids
- Molecular mass:
- 56651 Da
- Quaternary structure:
-
- Homotetramer.
Protein Expression for PHGDH Gene
Selected DME Specific Peptides for PHGDH Gene
- O43175:
-
- PHLGAST
- TFAQCKKGV
- GREVATR
- ADVNLVNAKLL
- ILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKV
- LNGAVFRPEVPL
- CLSPAVIVGLL
- MLPTMIGLLAEA
- IWPLCDFITVHTPLLPSTTGLLND
- AWAGSPKG
- LVMNTPNGNSLSAAELTCGM
- TQGTSLKN
- VSDGETWHVM
- HVTEAFQF
- ARGGIVDE
- LLSYQTS
- EAQSRCGEEIA
- VALAGAPYQAVGLVQGT
- GMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHT
Post-translational modifications for PHGDH Gene
Other Protein References for PHGDH Gene
- ENSEMBL proteins:
-
- ENSP00000493382
- ENSP00000493433
- ENSP00000492948
- ENSP00000493175
- ENSP00000493415
- ENSP00000492994
- ENSP00000493079
- ENSP00000493446
- ENSP00000493264
- ENSP00000493187
- ENSP00000358417
- ENSP00000493398
- ENSP00000493453
- ENSP00000493213
- ENSP00000493288
- ENSP00000493089
- ENSP00000493305
- ENSP00000493432
- ENSP00000492955
- ENSP00000493147
- ENSP00000493296
- REFSEQ proteins:
Antibody Products
- G Biosciences Immunotag™ PHGDH Antibody
- NSJ Bioreagents PHGDH Antibody
-
Custom Antibody ServicesOriGene Antibodies for PHGDH
- Novus Biologicals Antibodies for PHGDH
-
Abcam antibodies for PHGDH
- Invitrogen Antibodies for PHGDH (AFLGC-PHGDH)
-
Boster Bio Antibodies for PHGDH
-
Santa Cruz Biotechnology (SCBT) Antibodies for PHGDH
- Sino Biological Antibodies for PHGDH
Protein Products
- Search Origene for MassSpec and Protein Over-expression Lysates for PHGDH
- Origene Custom Protein Services for PHGDH
- Sino Biological Recombinant Proteins for PHGDH
- Browse Sino Biological Cell Lysates
-
Abcam proteins for PHGDH
Domains & Families for PHGDH Gene
Gene Families for PHGDH Gene
- Human Protein Atlas (HPA):
-
- Disease related genes
- Enzymes
- Plasma proteins
- Potential drug targets
- Predicted intracellular proteins
Protein Domains for PHGDH Gene
- InterPro:
- Blocks:
-
- Casein, alpha/beta
- D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
- ProtoNet:
Suggested Antigen Peptide Sequences for PHGDH Gene
- GenScript: Design optimal peptide antigens:
-
- PHGDH protein (Q8N5M8_HUMAN)
- 3-phosphoglycerate dehydrogenase (Q9UMY2_HUMAN)
- 3-phosphoglycerate dehydrogenase (Q9UMY3_HUMAN)
- D-3-phosphoglycerate dehydrogenase (SERA_HUMAN)
Graphical View of Domain Structure for InterPro Entry
O43175UniProtKB/Swiss-Prot:
SERA_HUMAN :- Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
- Family:
-
- Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
Function for PHGDH Gene
Molecular function for PHGDH Gene
- UniProtKB/Swiss-Prot Function:
- Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
- UniProtKB/Swiss-Prot CatalyticActivity:
- Reaction=(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + H(+) + NADH; Xref=Rhea:RHEA:12641, ChEBI:CHEBI:15378, ChEBI:CHEBI:18110, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:58272; EC=1.1.1.95; Evidence={ECO:0000269|PubMed:11751922};.
- UniProtKB/Swiss-Prot CatalyticActivity:
- Reaction=(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + H(+) + NADH; Xref=Rhea:RHEA:49612, ChEBI:CHEBI:15378, ChEBI:CHEBI:15801, ChEBI:CHEBI:16810, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.399; Evidence={ECO:0000269|PubMed:25406093};.
- UniProtKB/Swiss-Prot CatalyticActivity:
- Reaction=(S)-malate + NAD(+) = H(+) + NADH + oxaloacetate; Xref=Rhea:RHEA:21432, ChEBI:CHEBI:15378, ChEBI:CHEBI:15589, ChEBI:CHEBI:16452, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.37; Evidence={ECO:0000269|PubMed:25406093};.
- UniProtKB/Swiss-Prot Induction:
- Induced by 17-beta-estradiol (estrogenic ligand) and 4-hydroxytamoxifen (agonist/antagonist ligand). Positively regulated by the transcription factors SP1 and NF-Y.
- UniProtKB/Swiss-Prot BiophysicochemicalProperties:
- Kinetic parameters: KM=21.6 uM for 3-phosphonooxypyruvate {ECO:0000269|PubMed:19235232}; KM=0.26 mM for 3-phosphoglycerate {ECO:0000269|PubMed:25406093}; KM=6.5 mM for oxaloacetate {ECO:0000269|PubMed:25406093}; KM=10.1 mM for 2-oxoglutarate {ECO:0000269|PubMed:25406093}; KM=22 uM for NAD(+) {ECO:0000269|PubMed:25406093}; KM=4 uM for NADH {ECO:0000269|PubMed:25406093}; Vmax=35 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in patient-derived fibroblasts) {ECO:0000269|PubMed:19235232}; Vmax=168 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in 3-PGDH overexpressed cells) {ECO:0000269|PubMed:19235232}; Note=kcat is 4.5 min(-1) for 3-phosphoglycerate oxidation. kcat is 10.6 min(-1) for oxaloacetate reduction. kcat is 4.7 min(-1) for 2-oxoglutarate reduction. {ECO:0000269|PubMed:25406093};
Enzyme Numbers (IUBMB) for PHGDH Gene
Phenotypes From GWAS Catalog for PHGDH Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0004617 | phosphoglycerate dehydrogenase activity | IEA,IBA | 21873635 |
| GO:0009055 | electron transfer activity | TAS | 8758134 |
| GO:0016491 | oxidoreductase activity | IEA | -- |
| GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA | -- |
| GO:0030060 | L-malate dehydrogenase activity | IEA | -- |
Phenotypes for PHGDH Gene
- MGI mutant phenotypes for PHGDH:
- inferred from 3 alleles
- GenomeRNAi human phenotypes for PHGDH:
Animal Models for PHGDH Gene
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for PHGDH - Select products 50% OFF >
- * PHGDH CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
-
OriGene CRISPR knockouts for PHGDH
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for PHGDH
-
Santa Cruz Biotechnology (SCBT) CRISPR for PHGDH
miRNA for PHGDH Gene
- miRTarBase miRNAs that target PHGDH
-
- hsa-miR-155-5p (MIRT020945)
- hsa-miR-26b-5p (MIRT030040)
- hsa-miR-1229-3p (MIRT036377)
- hsa-miR-296-3p (MIRT038390)
- hsa-miR-615-3p (MIRT039728)
- hsa-miR-331-3p (MIRT043507)
- hsa-miR-107 (MIRT048300)
- hsa-miR-143-5p (MIRT265755)
- hsa-miR-759 (MIRT265756)
- hsa-miR-4519 (MIRT265758)
- hsa-miR-6499-3p (MIRT265759)
- hsa-miR-6792-5p (MIRT265760)
- hsa-miR-6733-3p (MIRT332444)
- hsa-miR-1178-5p (MIRT367150)
- hsa-miR-6801-5p (MIRT367151)
- hsa-miR-4257 (MIRT571069)
- hsa-miR-6847-5p (MIRT571070)
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for PHGDH
- Browse OriGene Inhibitory RNA Products For PHGDH
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHGDH
Clone Products
- Applied Biological Materials (abm): Clones for PHGDH - Select products 50% OFF >
- * PHGDH as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Sino Biological Human cDNA Clone for PHGDH
- Addgene plasmids for PHGDH
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for PHGDH
Cell Line Products
-
Horizon Cell Lines for PHGDH
No data available for Transcription Factor Targets and HOMER Transcription for PHGDH Gene
Localization for PHGDH Gene
| Compartment | Confidence |
|---|---|
| cytosol | 5 |
| extracellular | 4 |
| nucleus | 4 |
| plasma membrane | 3 |
| cytoskeleton | 3 |
| mitochondrion | 3 |
| endoplasmic reticulum | 3 |
| peroxisome | 2 |
| endosome | 2 |
| lysosome | 2 |
| golgi apparatus | 2 |
- Cytosol (4)
- Plasma membrane (4)
- Nucleoplasm (2)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005829 | cytosol | TAS | -- |
| GO:0070062 | extracellular exosome | HDA | 19056867 |
No data available for Subcellular locations from UniProtKB/Swiss-Prot for PHGDH Gene
Pathways & Interactions for PHGDH Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Carbon metabolism | ||
| 2 | Metabolism |
.40
|
|
| 3 | Amino acid synthesis and interconversion (transamination) | ||
| 4 | Glucose / Energy Metabolism | ||
| 5 | Sulfur amino acid metabolism | ||
Pathways by source for PHGDH Gene
1 BioSystems pathway for PHGDH Gene
4 Reactome pathways for PHGDH Gene
5 KEGG pathways for PHGDH Gene
1 Cell Signaling Technology pathway for PHGDH Gene
UniProtKB/Swiss-Prot O43175-SERA_HUMAN
- Pathway: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3.
Interacting Proteins for PHGDH Gene
GPS-Prot Interaction Network for PHGDH
SIGNOR curated interactions for PHGDH Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006520 | cellular amino acid metabolic process | IBA | 21873635 |
| GO:0006541 | glutamine metabolic process | IEA | -- |
| GO:0006544 | glycine metabolic process | IEA | -- |
| GO:0006563 | L-serine metabolic process | IEA | -- |
| GO:0006564 | L-serine biosynthetic process | IEA,TAS | -- |
Drugs & Compounds for PHGDH Gene
| Name | Status | Disease Links | Group | Role | Mechanism of Action | Clinical Trials |
|---|---|---|---|---|---|---|
| NADH | Approved | Nutra | Target | 0 | ||
| D-tartaric acid | Experimental | Pharma | Target | 0 | ||
| 3-Phosphoglyceric acid | Experimental | Pharma | 0 | |||
| NAD | Experimental | Pharma | Agonist, Full agonist, Activator | 0 | ||
| Oxogluric acid | Experimental, Investigational | Nutra | 0 |
| Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
|---|---|---|---|---|---|---|
| 2-hydroxyglutarate |
|
|
||||
| D-2-Hydroxyglutaric acid |
|
13095-47-1 |
|
|||
| Hydrogen Ion |
|
|
||||
| Phosphohydroxypyruvic acid |
|
3913-50-6 |
|
(1) ApexBio Compounds for PHGDH Gene
| Compound | Action | Cas Number |
|---|---|---|
| CBR-5884 | selective inhibitor of PHGDH |
Transcripts for PHGDH Gene
mRNA/cDNA for PHGDH Gene
- 1 REFSEQ mRNAs :
- 17 NCBI additional mRNA sequence :
- 34 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000369407 3180 nts (view in UCSC)
- ENST00000369409 1882 nts (view in UCSC)
- ENST00000462324 767 nts (view in UCSC)
- ENST00000469443 653 nts (view in UCSC)
- ENST00000482968 1754 nts (view in UCSC)
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for PHGDH - Select products 50% OFF >
- * PHGDH CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
-
OriGene CRISPR knockouts for PHGDH
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for PHGDH
-
Santa Cruz Biotechnology (SCBT) CRISPR for PHGDH
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for PHGDH
- Browse OriGene Inhibitory RNA Products For PHGDH
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHGDH
Clone Products
- Applied Biological Materials (abm): Clones for PHGDH - Select products 50% OFF >
- * PHGDH as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Sino Biological Human cDNA Clone for PHGDH
- Addgene plasmids for PHGDH
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for PHGDH
| ExUns: | 1a | · | 1b | · | 1c | ^ | 2 | ^ | 3a | · | 3b | ^ | 4a | · | 4b | · | 4c | ^ | 5a | · | 5b | ^ | 6 | ^ | 7 | ^ | 8a | · | 8b | ^ | 9a | · | 9b | · | 9c | ^ | 10 | ^ | 11a | · | 11b | · | 11c | ^ | 12a | · | 12b | ^ | 13a | · | 13b | ^ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | - | - | - | - | - | - | - | |||||||||||||||||||||||||||||||||||||||||||||
| SP2: | - | - | - | - | - | |||||||||||||||||||||||||||||||||||||||||||||||
| SP3: | - | - | - | - | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||
| SP4: | - | - | - | - | - | - | - | - | - | |||||||||||||||||||||||||||||||||||||||||||
| SP5: | - | - | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||
| SP6: | - | - | - | - | - | - | - | - | - | |||||||||||||||||||||||||||||||||||||||||||
| SP7: | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||
| SP8: | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||||
| SP9: | - | - | - | - | ||||||||||||||||||||||||||||||||||||||||||||||||
| SP10: | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |||||||||||||||||||||||||||||||
| SP11: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| SP12: | - | - | - | |||||||||||||||||||||||||||||||||||||||||||||||||
| SP13: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| SP14: | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| SP15: |
| ExUns: | 14a | · | 14b | ^ | 15 | ^ | 16a | · | 16b | ^ | 17a | · | 17b | · | 17c |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SP1: | - | - | |||||||||||||
| SP2: | - | - | |||||||||||||
| SP3: | |||||||||||||||
| SP4: | |||||||||||||||
| SP5: | |||||||||||||||
| SP6: | |||||||||||||||
| SP7: | |||||||||||||||
| SP8: | |||||||||||||||
| SP9: | |||||||||||||||
| SP10: | - | ||||||||||||||
| SP11: | - | - | - | - | - | ||||||||||
| SP12: | |||||||||||||||
| SP13: | - | ||||||||||||||
| SP14: | |||||||||||||||
| SP15: |
Relevant External Links for PHGDH Gene
- GeneLoc Exon Structure for
- PHGDH
Expression for PHGDH Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
-
Brain (Nervous System)
- Bergmann Glia Purkinje Cell Layer
- Protoplasmic Astrocyte Cells Neocortex
- Hypothalamus
- Pituitary Gland
- Thalamus
- Neural Tube (Nervous System)
-
Glial Cells
- Bergmann Glia Purkinje Cell Layer
- Protoplasmic Astrocyte Cells Neocortex
- NULL (Uncategorized)
-
Eye (Sensory Organs)
- Lens Vesicle Cells Lens Vesicle
- Gut Tube (Gastrointestinal Tract)
- Kidney (Urinary System)
- Thymus (Hematopoietic System)
- Adipose (Muscoskeletal System)
-
Prostate (Endocrine System)
-
Lymph (Hematopoietic System)
This gene is overexpressed in Bone (14.8).
Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHGDH Gene
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHGDH
SOURCE GeneReport for Unigene cluster for PHGDH Gene:
Hs.487296Evidence on tissue expression from TISSUES for PHGDH Gene
- Nervous system(5)
- Lung(4.9)
- Liver(4.8)
- Muscle(4.7)
- Blood(4.6)
- Kidney(4.4)
- Skin(4.3)
- Eye(4.3)
- Intestine(3.7)
- Heart(3.1)
- Thyroid gland(2.9)
- Pancreas(2.9)
- Stomach(2.4)
- Lymph node(2.3)
- Bone(2.2)
- Spleen(2.2)
- Bone marrow(2.1)
- Adrenal gland(2.1)
- Urine(2.1)
Phenotype-based relationships between genes and organs from Gene ORGANizer for PHGDH Gene
Germ Layers:
- ectoderm
- endoderm
- mesoderm
Systems:
- cardiovascular
- digestive
- integumentary
- nervous
- reproductive
- respiratory
- skeletal muscle
- skeleton
- urinary
Regions:
Head and neck:
- brain
- cerebellum
- chin
- ear
- eye
- eyelid
- face
- forehead
- head
- jaw
- lip
- mandible
- maxilla
- mouth
- neck
- nose
- outer ear
- skull
Thorax:
- heart
- lung
- rib
- rib cage
Abdomen:
- kidney
Pelvis:
- pelvis
- penis
- placenta
- testicle
- ureter
- uterus
- vagina
- vulva
Limb:
- ankle
- arm
- digit
- femur
- fibula
- finger
- foot
- forearm
- hand
- humerus
- lower limb
- radius
- shin
- shoulder
- thigh
- tibia
- toe
- ulna
- upper limb
General:
- blood
- blood vessel
- coagulation system
- hair
- peripheral nerve
- peripheral nervous system
- red blood cell
- skin
- spinal column
- spinal cord
- vertebrae
Primer Products
-
OriGene qPCR primer pairs for PHGDH
-
OriGene qPCR primer pairs and template standards for PHGDH
Gene Expression Assay Products
No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PHGDH Gene
Orthologs for PHGDH Gene
This gene was present in the common ancestor of eukaryotes.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | PHGDH 30 31 |
|
OneToOne | |
| Dog (Canis familiaris) |
Mammalia | -- 31 |
|
OneToMany | |
| LOC607890 30 |
|
||||
| -- 31 |
|
OneToMany | |||
| -- 31 |
|
OneToMany | |||
| Rat (Rattus norvegicus) |
Mammalia | Phgdh 30 |
|
||
| Cow (Bos Taurus) |
Mammalia | PHGDH 30 31 |
|
OneToOne | |
| Mouse (Mus musculus) |
Mammalia | Phgdh 30 17 31 |
|
OneToOne | |
| Oppossum (Monodelphis domestica) |
Mammalia | PHGDH 31 |
|
OneToOne | |
| Platypus (Ornithorhynchus anatinus) |
Mammalia | PHGDH 31 |
|
OneToOne | |
| Chicken (Gallus gallus) |
Aves | PHGDH 30 31 |
|
OneToOne | |
| Lizard (Anolis carolinensis) |
Reptilia | PHGDH 31 |
|
OneToOne | |
| Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | phgdh 30 |
|
||
| Str.20062 30 |
|
||||
| Zebrafish (Danio rerio) |
Actinopterygii | phgdh 30 31 |
|
OneToOne | |
| wufb38f06 30 |
|
||||
| African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP008849 30 |
|
||
| Fruit Fly (Drosophila melanogaster) |
Insecta | CG6287 30 31 32 |
|
OneToOne | |
| Worm (Caenorhabditis elegans) |
Secernentea | CELE_C31C9.2 30 |
|
||
| C31C9.2 31 32 |
|
OneToOne | |||
| Baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | SER33 31 33 |
|
ManyToMany | |
| SER3 31 |
|
ManyToMany | |||
| Thale Cress (Arabidopsis thaliana) |
eudicotyledons | EDA9 30 |
|
||
| Rice (Oryza sativa) |
Liliopsida | Os04g0650800 30 |
|
||
| Sea Squirt (Ciona savignyi) |
Ascidiacea | CSA.6094 31 |
|
OneToOne | |
| Sea Vase (Ciona intestinalis) |
Ascidiacea | Cin.4899 30 |
|
- Species where no ortholog for PHGDH was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Eremothecium gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- African clawed frog (Xenopus laevis)
- Alicante grape (Vitis vinifera)
- Alpha proteobacteria (Wolbachia pipientis)
- Amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- Barley (Hordeum vulgare)
- Beta proteobacteria (Neisseria meningitidis)
- Bread mold (Neurospora crassa)
- Chromalveolata (Phytophthora infestans)
- Common water flea (Daphnia pulex)
- Corn (Zea mays)
- E. coli (Escherichia coli)
- Filamentous fungi (Aspergillus nidulans)
- Firmicute Bacteria (Streptococcus pneumoniae)
- Fission Yeast (Schizosaccharomyces pombe)
- Green Algae (Chlamydomonas reinhardtii)
- Honey Bee (Apis mellifera)
- K. Lactis Yeast (Kluyveromyces lactis)
- Loblloly Pine (Pinus taeda)
- Malaria Parasite (Plasmodium falciparum)
- Medicago Trunc (Medicago Truncatula)
- Moss (Physcomitrella patens)
- Orangutan (Pongo pygmaeus)
- Pig (Sus scrofa)
- Rainbow Trout (Oncorhynchus mykiss)
- Rice Blast Fungus (Magnaporthe grisea)
- Schistosome Parasite (Schistosoma mansoni)
- Sea Anemone (Nematostella vectensis)
- Sea Urchin (Strongylocentrotus purpuratus)
- Sorghum (Sorghum bicolor)
- Soybean (Glycine max)
- Stem Rust Fungus (Puccinia graminis)
- Sugarcane (Saccharum officinarum)
- Tomato (Lycopersicon esculentum)
- Toxoplasmosis (Toxoplasma gondii)
- Trichoplax (Trichoplax adhaerens)
- Wheat (Triticum aestivum)
Evolution for PHGDH Gene
- ENSEMBL:
- Gene Tree for PHGDH (if available)
- TreeFam:
- Gene Tree for PHGDH (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for PHGDH: view image
Paralogs for PHGDH Gene
Variants for PHGDH Gene
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PHGDH Gene
| SNP ID | Clinical significance and condition | Chr 01 pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| 644494 | Uncertain Significance: Phosphoglycerate dehydrogenase deficiency | 119,712,090(+) | T/G | MISSENSE_VARIANT | |
| 646848 | Uncertain Significance: Phosphoglycerate dehydrogenase deficiency | 119,735,439(+) | C/T | MISSENSE_VARIANT | |
| 647932 | Uncertain Significance: Phosphoglycerate dehydrogenase deficiency | 119,741,784(+) | G/T | MISSENSE_VARIANT | |
| 656320 | Uncertain Significance: Phosphoglycerate dehydrogenase deficiency | 119,740,386(+) | G/A | MISSENSE_VARIANT | |
| 657985 | Uncertain Significance: Phosphoglycerate dehydrogenase deficiency | 119,735,358(+) | G/A | MISSENSE_VARIANT |
Residual Variation Intolerance Score:
17.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
1.98;
36.63% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for PHGDH Gene
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHGDH Gene
Disorders for PHGDH Gene
(17) MalaCards diseases for PHGDH Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| phosphoglycerate dehydrogenase deficiency |
|
|
| neu-laxova syndrome 1 |
|
|
| visual epilepsy |
|
|
| serine deficiency |
|
|
| phosphoserine phosphatase deficiency |
|
|
Search PHGDH in MalaCards
View complete list of genes associated with diseases
UniProtKB/Swiss-Prot
SERA_HUMAN- Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815]: An autosomal recessive inborn error of L-serine biosynthesis, clinically characterized by congenital microcephaly, psychomotor retardation, and seizures. {ECO:0000269 PubMed:11055895, ECO:0000269 PubMed:19235232}. Note=The disease is caused by mutations affecting the gene represented in this entry.
- Neu-Laxova syndrome 1 (NLS1) [MIM:256520]: A lethal, autosomal recessive multiple malformation syndrome characterized by ichthyosis, marked intrauterine growth restriction, microcephaly, short neck, limb deformities, hypoplastic lungs, edema, and central nervous system anomalies including lissencephaly, cerebellar hypoplasia and/or abnormal/agenesis of the corpus callosum. Abnormal facial features include severe proptosis with ectropion, hypertelorism, micrognathia, flattened nose, and malformed ears. {ECO:0000269 PubMed:24836451}. Note=The disease is caused by mutations affecting the gene represented in this entry.
Additional Disease Information for PHGDH
- Genetic Association Database
- (GAD)
- Human Genome Epidemiology Navigator
- (HuGE)
- ATLAS of Genetics and Cytogenetics in Oncology and Haematology
- Open Targets Platform
No data available for Genatlas for PHGDH Gene
Publications for PHGDH Gene
- Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. (PMID: 19235232) Tabatabaie L … Klomp LW (Human mutation 2009) 3 4 23
- V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. (PMID: 11751922) Pind S … Natowicz MR (The Journal of biological chemistry 2002) 3 4 23
- Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene. (PMID: 10713460) Cho HM … Kim YH (Gene 2000) 3 4 23
- Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency--a neurometabolic disorder associated with reduced L-serine biosynthesis. (PMID: 11055895) Klomp LW … Berger R (American journal of human genetics 2000) 3 4 23
- Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH. (PMID: 24836451) Shaheen R … Alkuraya FS (American journal of human genetics 2014) 3 4
ExternalLinks
Products for PHGDH Gene
- Custom Antibody ServicesOriGene Antibodies for PHGDH
- Browse OriGene ELISA Kits
- Custom Assay Services
- Search Origene for MassSpec and Protein Over-expression Lysates for PHGDH
- Origene Custom Protein Services for PHGDH
- Origene shrna, sirna, and RNAi products in human, mouse, rat for PHGDH
- Browse OriGene Inhibitory RNA Products For PHGDH
- OriGene qPCR primer pairs for PHGDH
- OriGene qPCR primer pairs and template standards for PHGDH
- OriGene CRISPR knockouts for PHGDH
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Browse OriGene miRNA Products For PHGDH
- Sino Biological Human cDNA Clone for PHGDH
- Sino Biological Recombinant Proteins for PHGDH
- Browse Sino Biological Cell Lysates
- Sino Biological Antibodies for PHGDH
- Browse Sino Biological Assays
- Browse Recombinant Proteins
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- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Novus Biologicals Antibodies for PHGDH
- Novus Biologicals proteins and lysates for PHGDH
- Browse Antibodies
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- Abcam antibodies for PHGDH
- Abcam proteins for PHGDH
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- Invitrogen Antibodies for PHGDH (AFLGC-PHGDH)
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- VectorBuilder Custom and pre-made DNA vectors for PHGDH (ie. gene expression, shRNA knockdown, CRISPR)
- VectorBuilder Viral vectors for PHGDH (ie. lentivirus, AAV, adenovirus)
- VectorBuilder CRISPR vectors for PHGDH (ie. knockout, knockin, CRISPRa, CRISPRi)
- VectorBuilder Virus packaging for PHGDH CRISPR vectors (ie. lentivirus, AAV, adenovirus)
- VectorBuilder Stable cell line generation for PHGDH
- Addgene plasmids for PHGDH
- antibodies-online: Show 149 available Pregnanediol-3-Glucuronide (PDG) Antibodies ranked by validation data
- Compare Top Pregnanediol-3-Glucuronide (PDG) Antibodies
- antibodies-online: Show 10 available Pregnanediol-3-Glucuronide (PDG) Elisa Kits ranked by validation data
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- Quality Products:
- antibodies-online: Show 11 available Pregnanediol-3-Glucuronide (PDG) Proteins ranked by validation data
- Compare Top Pregnanediol-3-Glucuronide (PDG) Proteins
- Santa Cruz Biotechnology (SCBT) Antibodies for PHGDH
- Search Santa Cruz Biotechnology (SCBT) for PHGDH siRNA/shRNA
- Santa Cruz Biotechnology (SCBT) CRISPR for PHGDH
- Horizon Cell Lines for PHGDH
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for PHGDH
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for PHGDH
- Search GeneCopoeia for miRNA 3'UTR Target clone products for PHGDH
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHGDH
- Boster Bio Antibodies for PHGDH
- Browse Boster Bio ELISA Kits
Sources for PHGDH Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) Genetics Home Reference
- (111) MeSH
- (112) MedlinePlus
- (113) CDC
- (114) NINDS
- (115) NCBI Bookshelf
- (116) ClinVar
- (117) Gene Damage Index
- (118) HPO
- (119) UDN
- (120) VISTA
- (121) FANTOM5
- (122) ENCODE
- (123) ProSci
- (124) Horizon
- (125) The Signaling Pathways Project (SPP)
- (126) IID
- (127) VectorBuilder
- (128) SNPedia
- (129) BRCA Exchange
- (130) CIViC
- (131) ProteoGenix
- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNACentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Signalway Antibody
- (175) Open Targets Platform
- (176) 5SRRNADB
- (177) snoDB
- (178) MirGeneDB