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PHGDH Gene(Protein Coding)

Phosphoglycerate Dehydrogenase

GCID:
GC01P119660
GIFtS:
59
Genes Participants
UDN Logo

Aliases for PHGDH Gene

Aliases for PHGDH Gene

  • Phosphoglycerate Dehydrogenase 2 3 5
  • 2-Oxoglutarate Reductase 3 4
  • Malate Dehydrogenase 3 4
  • EC 1.1.1.95 4 56
  • 3-PGDH 3 4
  • Epididymis Secretory Protein Li 113 3
  • D-3-Phosphoglycerate Dehydrogenase 3
  • 3-Phosphoglycerate Dehydrogenase 3
  • EC 1.1.1.399 4
  • EC 1.1.1.37 4
  • HEL-S-113 3
  • EC 1.1.1 56
  • PHGDHD 3
  • 3PGDH 3
  • PGDH3 4
  • PGDH 3
  • NLS1 3
  • PGAD 3
  • SERA 3
  • NLS 3
  • PDG 3
  • PGD 3

External Ids for PHGDH Gene

Previous GeneCards Identifiers for PHGDH Gene

  • GC01P120701
  • GC01P119092
  • GC01P119401
  • GC01P119600
  • GC01P119966
  • GC01P120056
  • GC01P120202
  • GC01P118112

Summaries for PHGDH Gene

Entrez Gene Summary 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 Viral mRNA Translation and Metabolism. 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 CTBP1.

UniProtKB/Swiss-Prot 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.

Tocris Summary for PHGDH Gene

Gene Wiki entry for PHGDH Gene

Additional gene information for PHGDH Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHGDH Gene

Genomics for PHGDH Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PHGDH Gene

Promoters and enhancers for PHGDH Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01I119711 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 577.2 +64.7 64698 3.6 PKNOX1 SMAD1 SIN3A FEZF1 DMAP1 ZNF2 POLR2B ZNF766 ZNF213 KLF13 PHGDH LOC105378937 ADAM30 ZNF697 LOC105378936
GH01I119645 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 -1.1 -1075 3.9 HDGF ARNT ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 ZNF143 FOS ZNF697 PHGDH GC01M119620
GH01I119723 Enhancer 0.9 ENCODE 26.9 +76.6 76641 2.3 FOXA2 MLX ARID4B ETS1 ATF7 SP5 MIER2 KAT8 NFIL3 SSRP1 PHGDH ZNF697 HMGCS2 LINC00622 LOC105378936 LOC105378937
GH01I119782 Enhancer 1.3 Ensembl ENCODE dbSUPER 18.1 +137.3 137260 6.9 PKNOX1 FOXA2 RAD21 RFX5 RARA YY1 ZNF766 ZNF366 FOS RXRA PHGDH WARS2 REG4 HMGCS2 ADAM30 LOC101929147
GH01I119686 Enhancer 0.8 Ensembl ENCODE 18.2 +38.8 38844 1.9 SMARCE1 USF1 CEBPB CEBPG DPF2 SP1 MITF CTBP1 POU5F1 CUX1 ZNF697 PHGDH LOC105378937
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHGDH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHGDH gene promoter:

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)

Genomic View for PHGDH Gene

Genes around PHGDH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHGDH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHGDH Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PHGDH Gene

Proteins for PHGDH Gene

Products:

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  2. Protein
  3. Assay

  • Protein details for PHGDH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43175-SERA_HUMAN
    Recommended name:
    D-3-phosphoglycerate dehydrogenase
    Protein Accession:
    O43175
    Secondary Accessions:
    • B2RD08
    • Q5SZU3
    • Q9BQ01

    Protein attributes for PHGDH Gene

    Size:
    533 amino acids
    Molecular mass:
    56651 Da
    Quaternary structure:
    • Homotetramer.

    Three dimensional structures from OCA and Proteopedia for PHGDH Gene

neXtProt entry for PHGDH Gene

Protein Expression for PHGDH Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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

  • Ubiquitination at Lys21, Lys38, isoforms=146, Lys289, Lys351, Lys364, isoforms=380, and Lys384
  • Modification sites at PhosphoSitePlus

Other Protein References for PHGDH Gene

ENSEMBL proteins:
REFSEQ proteins:

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:
ProtoNet:

Suggested Antigen Peptide Sequences for PHGDH Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O43175

UniProtKB/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.
genes like me logo Genes that share domains with PHGDH: view

Function for PHGDH Gene

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  1. Animal Model
  2. CRISPR
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  6. Cell Line

Molecular function for PHGDH Gene

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};
UniProtKB/Swiss-Prot CatalyticActivity:
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH.
UniProtKB/Swiss-Prot CatalyticActivity:
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH.
UniProtKB/Swiss-Prot CatalyticActivity:
(S)-malate + NAD(+) = oxaloacetate + NADH.
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 Induction:
Induced by 17-beta-estradiol (estrogenic ligand) and 4-hydroxytamoxifen (agonist/antagonist ligand). Positively regulated by the transcription factors SP1 and NF-Y.

Enzyme Numbers (IUBMB) for PHGDH Gene

Phenotypes From GWAS Catalog for PHGDH Gene

Gene Ontology (GO) - Molecular Function for PHGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004617 phosphoglycerate dehydrogenase activity TAS --
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 --
genes like me logo Genes that share ontologies with PHGDH: view
genes like me logo Genes that share phenotypes with PHGDH: view

Human Phenotype Ontology for PHGDH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PHGDH Gene

MGI Knock Outs for PHGDH:

Animal Model Products

Clone Products

  • Addgene plasmids for PHGDH

No data available for Transcription Factor Targets and HOMER Transcription for PHGDH Gene

Localization for PHGDH Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHGDH gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 4
plasma membrane 3
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleoplasm (4)
  • Plasma membrane (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PHGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0043209 myelin sheath IDA --
GO:0070062 extracellular exosome IDA,HDA 19056867
genes like me logo Genes that share ontologies with PHGDH: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PHGDH Gene

Pathways & Interactions for PHGDH Gene

genes like me logo Genes that share pathways with PHGDH: view

UniProtKB/Swiss-Prot O43175-SERA_HUMAN

  • Pathway: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3.

Gene Ontology (GO) - Biological Process for PHGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006541 glutamine metabolic process IMP --
GO:0006544 glycine metabolic process IMP --
GO:0006563 L-serine metabolic process IMP --
GO:0006564 L-serine biosynthetic process TAS --
GO:0006566 threonine metabolic process IMP --
genes like me logo Genes that share ontologies with PHGDH: view

No data available for SIGNOR curated interactions for PHGDH Gene

Drugs & Compounds for PHGDH Gene

Products:

  1. Drug

(6) Drugs for PHGDH Gene - From: DrugBank, ApexBio, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NADH Approved Nutra Target 0
3-Phosphoglyceric acid Experimental Pharma 0
CBR-5884 Pharma selective inhibitor of PHGDH 0
NAD Pharma Full agonist, Agonist 0

(10) Additional Compounds for PHGDH Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
2-hydroxyglutarate
D-2-Hydroxyglutaric acid
  • (R)-2-hydroxy-Pentanedioate
  • (R)-2-hydroxy-Pentanedioic acid
  • (R)-2-Hydroxyglutarate
  • (R)-2-Hydroxyglutaric acid
  • (R)-a-Hydroxyglutarate
 2889-31-8
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
 328-50-7
Phosphohydroxypyruvic acid
  • 2-Oxo-3-(phosphonooxy)-Propanoate
  • 2-Oxo-3-(phosphonooxy)-Propanoic acid
  • 3-Phosphohydroxypyruvate
  • 3-Phosphohydroxypyruvic acid
  • 3-Phosphonatooxypyruvate
 3913-50-6

(1) ApexBio Compounds for PHGDH Gene

Compound Action Cas Number
CBR-5884 selective inhibitor of PHGDH
genes like me logo Genes that share compounds with PHGDH: view

Drug Products

Transcripts for PHGDH Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PHGDH Gene

(5) REFSEQ mRNAs :
(14) Additional mRNA sequences :
(1066) Selected AceView cDNA sequences:
(34) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PHGDH Gene

Phosphoglycerate dehydrogenase:
Representative Sequences:

Clone Products

  • Addgene plasmids for PHGDH

Alternative Splicing Database (ASD) splice patterns (SP) for PHGDH Gene

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
ECgene alternative splicing isoforms for
PHGDH

Expression for PHGDH Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHGDH Gene

mRNA expression in normal human tissues for PHGDH Gene
mRNA expression by BioGPS for PHGDH GenemRNA expression by GTEx for PHGDH Gene

Protein differential expression in normal tissues from HIPED for PHGDH Gene

This gene is overexpressed in Bone (14.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHGDH Gene



Protein tissue co-expression partners for PHGDH Gene

NURSA nuclear receptor signaling pathways regulating expression of PHGDH Gene:

PHGDH

SOURCE GeneReport for Unigene cluster for PHGDH Gene:

Hs.487296

Evidence on tissue expression from TISSUES for PHGDH Gene

  • Nervous system(5)
  • Lung(4.8)
  • Liver(4.7)
  • Muscle(4.6)
  • Kidney(4.2)
  • Eye(4)
  • Skin(3.8)
  • Intestine(2.9)
  • Blood(2.6)
  • Heart(2.5)
  • Pancreas(2.3)
  • 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
genes like me logo Genes that share expression patterns with PHGDH: view

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.

Orthologs for PHGDH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PHGDH 33 34
  • 99.44 (n)
dog
(Canis familiaris)
 Mammalia -- 34
  • 92 (a)
 OneToMany
LOC607890 33
  • 89.49 (n)
-- 34
  • 86 (a)
 OneToMany
-- 34
  • 66 (a)
 OneToMany
rat
(Rattus norvegicus)
 Mammalia Phgdh 33
  • 88.24 (n)
cow
(Bos Taurus)
 Mammalia PHGDH 33 34
  • 88.12 (n)
mouse
(Mus musculus)
 Mammalia Phgdh 33 16 34
  • 88.06 (n)
oppossum
(Monodelphis domestica)
 Mammalia PHGDH 34
  • 87 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PHGDH 34
  • 83 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PHGDH 33 34
  • 68.83 (n)
lizard
(Anolis carolinensis)
 Reptilia PHGDH 34
  • 68 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia phgdh 33
  • 61.99 (n)
Str.20062 33
zebrafish
(Danio rerio)
 Actinopterygii phgdh 33 34
  • 64.88 (n)
wufb38f06 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP008849 33
  • 58.23 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG6287 35 33 34
  • 57.1 (n)
worm
(Caenorhabditis elegans)
 Secernentea CELE_C31C9.2 33
  • 57.67 (n)
C31C9.2 35 34
  • 53 (a)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes SER3 34
  • 27 (a)
 ManyToMany
SER33 34 36
  • 27 (a)
 ManyToMany
thale cress
(Arabidopsis thaliana)
 eudicotyledons EDA9 33
  • 51.94 (n)
rice
(Oryza sativa)
 Liliopsida Os04g0650800 33
  • 51.35 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.6094 34
  • 61 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4899 33
Species where no ortholog for PHGDH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for PHGDH Gene

Paralogs for PHGDH Gene

(2) SIMAP similar genes for PHGDH Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PHGDH: view

Variants for PHGDH Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for PHGDH Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1021309146 uncertain-significance, Phosphoglycerate dehydrogenase deficiency 119,711,840(+) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs115747918 likely-benign, Phosphoglycerate dehydrogenase deficiency 119,723,403(+) C/T 5_prime_UTR_variant, coding_sequence_variant, synonymous_variant
rs121907987 pathogenic, Phosphoglycerate dehydrogenase deficiency, Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815] 119,743,906(+) G/A coding_sequence_variant, missense_variant
rs121907988 pathogenic, Phosphoglycerate dehydrogenase deficiency, Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815] 119,742,870(+) G/A coding_sequence_variant, missense_variant
rs140037378 uncertain-significance, Phosphoglycerate dehydrogenase deficiency 119,744,206(+) /GTAG 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PHGDH Gene

Variant ID Type Subtype PubMed ID
nsv428201 CNV gain 18775914
nsv524681 CNV gain 19592680
nsv831204 CNV gain+loss 17160897
nsv831215 CNV gain 17160897

Variation tolerance for PHGDH Gene

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

Human Gene Mutation Database (HGMD)
PHGDH
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHGDH

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHGDH Gene

Disorders for PHGDH Gene

MalaCards: The human disease database

(12) MalaCards diseases for PHGDH Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
phosphoglycerate dehydrogenase deficiency
  • phgdhd
neu-laxova syndrome 1
  • nls1
serine deficiency
phosphoserine phosphatase deficiency
  • psphd
cerebral folate deficiency
  • neurodegeneration due to cerebral folate transport deficiency
- elite association - COSMIC cancer census association via MalaCards
Search PHGDH in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SERA_HUMAN
  • 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.
  • 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.

Additional Disease Information for PHGDH

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PHGDH: view

No data available for Genatlas for PHGDH Gene

Publications for PHGDH Gene

  1. 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 22 58
  2. 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 22 58
  3. Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene. (PMID: 10713460) Cho HM … Kim YH (Gene 2000) 3 4 22 58
  4. 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 22 58
  5. 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 58

Products for PHGDH Gene

  • Addgene plasmids for PHGDH

Sources for PHGDH Gene