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

  • Phosphoglycerate Dehydrogenase 2 3 5
  • D-3-Phosphoglycerate Dehydrogenase 2 3 4
  • 2-Oxoglutarate Reductase 3 4
  • Malate Dehydrogenase 3 4
  • EC 1.1.1.95 4 52
  • 3-PGDH 3 4
  • Epididymis Secretory Protein Li 113 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 52
  • PHGDHD 3
  • 3PGDH 3
  • PGDH3 4
  • NLS1 3
  • PGAD 3
  • PGDH 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 Amino acid synthesis and interconversion (transamination) and Carbon 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 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.

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 , Rfam classification and piRNA Summary for PHGDH Gene

Genomics for PHGDH Gene

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
GH01J119711 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 528.3 +64.9 64939 4.1 POLR2G GTF2E2 PHF8 ZNF639 REST POLR2A ZBTB10 ZBTB26 TARDBP SAP30 PHGDH LOC105378937 ADAM30 WARS2-AS1 ZNF697 LOC105378936
GH01J119645 Promoter/Enhancer 2 Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 -1.1 -1111 4.2 ZNF217 EP300 CTCF POLR2G GTF2E2 PHF8 JUND SIX5 FOS ZFX ZNF697 PHGDH lnc-ZNF697-2
GH01J119723 Enhancer 1.1 Ensembl ENCODE 26.9 +76.7 76736 2.5 EP300 FOXK2 NCOR1 KDM6A TCF7 ZBTB25 SKI TEAD1 TBX3 ZKSCAN8 PHGDH ZNF697 HMGCS2 LINC00622 LOC105378936 LOC105378937
GH01J119782 Enhancer 1.2 Ensembl ENCODE dbSUPER 18.1 +137.2 137156 7.1 RFX1 CUX1 TEAD1 ATF2 U2AF2 CTBP1 ZNF341 FOXA2 NR2F2 ESRRA HSALNG0006515 PHGDH REG4 HMGCS2 ADAM30 WARS2-AS1 WARS2
GH01J119686 Enhancer 0.8 Ensembl ENCODE 18.3 +39.4 39390 4 USF1 CUX1 CTBP1 ZNF316 MAFF CEBPG FOS CEBPB DPF2 MITF ZNF697 PHGDH piR-55194-023 LOC105378937
- 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 UCSC Golden Path with GeneCards custom track

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:
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 StructureGene 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
    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

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, Lys33, Lys38, Lys58, Lys146, Lys289, Lys351, Lys364, Lys380, Lys384, and Lys394
  • Modification sites at PhosphoSitePlus

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

Blocks:
  • Casein, alpha/beta
  • D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
InterPro:
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

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

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=. ;.
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=. ;.
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=. ;.
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 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 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 --
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:
  • Phgdh Phgdh<tm1.1Shfu>
  • Phgdh Phgdh<tm1b(KOMP)Wtsi>

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
cytosol 5
nucleus 4
plasma membrane 3
cytoskeleton 3
mitochondrion 3
endoplasmic reticulum 3
extracellular 2
peroxisome 2
endosome 2
lysosome 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Plasma membrane (4)
  • Nucleoplasm (2)
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:0070062 extracellular exosome 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.

SIGNOR curated interactions for PHGDH Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process 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 --
genes like me logo Genes that share ontologies with PHGDH: view

Drugs & Compounds for PHGDH Gene

(8) 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
D-tartaric acid Experimental Pharma Target 0
3-Phosphoglyceric acid Experimental Pharma 0
NAD Experimental Pharma Full agonist, Agonist, Activator 0
Oxogluric acid Experimental, Investigational Nutra 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
2-hydroxyglutarate
  • alpha-Hydroxyglutaric acid
  • a-Hydroxyglutarate
  • a-Hydroxyglutaric acid
  • alpha-Hydroxyglutarate
  • α-hydroxyglutarate
D-2-Hydroxyglutaric acid
  • (R)-2-Hydroxyglutarate
  • (R)-Hydroxyglutarate
  • (R)-2-Hydroxyglutaric acid
  • D-2-Hydroxyglutarate
  • (R)-Hydroxyglutaric acid
13095-47-1
Hydrogen Ion
  • H+
  • H(+)
  • Hydrogen cation
  • Hydron
  • Proton
Phosphohydroxypyruvic acid
  • 3-Phosphohydroxypyruvic acid
  • Hydroxypyruvic acid phosphate
  • 3-Phosphohydroxypyruvate
  • Phosphohydroxypyruvate
  • Hydroxypyruvate phosphate
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

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 :

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

Expression for PHGDH Gene

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



Protein tissue co-expression partners for PHGDH Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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 31 30
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia -- 31
  • 92 (a)
OneToMany
LOC607890 30
  • 89.49 (n)
-- 31
  • 86 (a)
OneToMany
-- 31
  • 66 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Phgdh 30
  • 88.24 (n)
cow
(Bos Taurus)
Mammalia PHGDH 31 30
  • 88.12 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Phgdh 17 31 30
  • 88.06 (n)
oppossum
(Monodelphis domestica)
Mammalia PHGDH 31
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHGDH 31
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHGDH 31 30
  • 68.83 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHGDH 31
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phgdh 30
  • 61.99 (n)
Str.20062 30
zebrafish
(Danio rerio)
Actinopterygii phgdh 31 30
  • 64.88 (n)
OneToOne
wufb38f06 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008849 30
  • 58.23 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6287 31 32 30
  • 57.1 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea CELE_C31C9.2 30
  • 57.67 (n)
C31C9.2 31 32
  • 53 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SER33 33 31
  • 27 (a)
SER3 31
  • 27 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons EDA9 30
  • 51.94 (n)
rice
(Oryza sativa)
Liliopsida Os04g0650800 30
  • 51.35 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6094 31
  • 61 (a)
OneToOne
Cin.4899 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4899 30
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)
Aminode:
Evolutionary constrained regions (ECRs) for PHGDH: view image

Paralogs for PHGDH Gene

Paralogs for PHGDH Gene

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

  • SERA_HUMAN
  • Q5SZU1_HUMAN
  • Q8N5M8_HUMAN
genes like me logo Genes that share paralogs with PHGDH: view

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

Additional dbSNP identifiers (rs#s) for PHGDH Gene

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

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

- 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
  • 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
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 23 54
  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 23 54
  3. 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 54
  4. Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene. (PMID: 10713460) Cho HM … Kim YH (Gene 2000) 3 4 23 54
  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 54

Products for PHGDH Gene

  • Addgene plasmids for PHGDH

Sources for PHGDH Gene