ENSG00000092621


Homo sapiens

Features
Gene ID: ENSG00000092621
  
Biological name :PHGDH
  
Synonyms : O43175 / PHGDH / phosphoglycerate dehydrogenase
  
Possible biological names infered from orthology :
  
Species: Homo sapiens
  
Chr. number: 1
Strand: 1
Band: p12
Gene start: 119648411
Gene end: 119744226
  
Corresponding Affymetrix probe sets: 201397_at (Human Genome U133 Plus 2.0 Array)   
  
Cross references: Ensembl peptide - ENSP00000493147
Ensembl peptide - ENSP00000493089
Ensembl peptide - ENSP00000493175
Ensembl peptide - ENSP00000493453
Ensembl peptide - ENSP00000493446
Ensembl peptide - ENSP00000493433
Ensembl peptide - ENSP00000493432
Ensembl peptide - ENSP00000493415
Ensembl peptide - ENSP00000493398
Ensembl peptide - ENSP00000493382
Ensembl peptide - ENSP00000493305
Ensembl peptide - ENSP00000493296
Ensembl peptide - ENSP00000493288
Ensembl peptide - ENSP00000493264
Ensembl peptide - ENSP00000493213
Ensembl peptide - ENSP00000493187
Ensembl peptide - ENSP00000358417
Ensembl peptide - ENSP00000492948
Ensembl peptide - ENSP00000492955
Ensembl peptide - ENSP00000492994
Ensembl peptide - ENSP00000493079
NCBI entrez gene - 26227     See in Manteia.
OMIM - 606879
RefSeq - XM_011541231
RefSeq - NM_006623
RefSeq - XM_011541226
RefSeq - XM_011541227
RefSeq - XM_011541228
RefSeq Peptide - NP_006614
swissprot - A0A286YFE1
swissprot - A0A286YFC8
swissprot - A0A286YFB2
swissprot - A0A286YFA2
swissprot - A0A286YF78
swissprot - A0A286YF34
swissprot - A0A286YF22
swissprot - A0A286YEZ0
swissprot - A0A286YER3
swissprot - O43175
swissprot - A0A2C9F2M7
swissprot - A0A286YFM8
swissprot - A0A286YFL2
swissprot - A0A286YFF3
swissprot - A0A286YFK5
Ensembl - ENSG00000092621
  
Related genetic diseases (OMIM): 256520 - Neu-Laxova syndrome 1, 256520
  601815 - Phosphoglycerate dehydrogenase deficiency, 601815
See expression report in BioGPS
See gene description in Wikigenes
See gene description in GeneCards
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 phgdhENSDARG00000001873Danio rerio
 PHGDHENSGALG00000002988Gallus gallus
 PhgdhENSMUSG00000053398Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
CTBP2 / P56545 / C-terminal binding protein 2ENSG0000017502923
CTBP1 / Q13363 / C-terminal binding protein 1ENSG0000015969222


Protein motifs (from Interpro)
Interpro ID Name
 IPR006139  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
 IPR006140  D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
 IPR006236  D-3-phosphoglycerate dehydrogenase
 IPR029009  Allosteric substrate binding domain superfamily
 IPR029752  D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1
 IPR029753  D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
 IPR036291  NAD(P)-binding domain superfamily


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0006541 glutamine metabolic process IEA
 biological_processGO:0006544 glycine metabolic process IEA
 biological_processGO:0006563 L-serine metabolic process IEA
 biological_processGO:0006564 L-serine biosynthetic process IEA
 biological_processGO:0006566 threonine metabolic process IEA
 biological_processGO:0007420 brain development TAS
 biological_processGO:0008152 metabolic process IEA
 biological_processGO:0008652 cellular amino acid biosynthetic process IEA
 biological_processGO:0009448 gamma-aminobutyric acid metabolic process IEA
 biological_processGO:0010468 regulation of gene expression IEA
 biological_processGO:0019530 taurine metabolic process IEA
 biological_processGO:0021510 spinal cord development IEA
 biological_processGO:0021782 glial cell development IEA
 biological_processGO:0021915 neural tube development IEA
 biological_processGO:0022008 neurogenesis IEA
 biological_processGO:0022900 electron transport chain IEA
 biological_processGO:0031175 neuron projection development IEA
 biological_processGO:0055114 oxidation-reduction process IEA
 biological_processGO:0070314 G1 to G0 transition IEA
 cellular_componentGO:0005829 cytosol TAS
 cellular_componentGO:0043209 myelin sheath IEA
 cellular_componentGO:0070062 extracellular exosome HDA
 molecular_functionGO:0004617 phosphoglycerate dehydrogenase activity IEA
 molecular_functionGO:0009055 electron transfer activity TAS
 molecular_functionGO:0016491 oxidoreductase activity IEA
 molecular_functionGO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IEA
 molecular_functionGO:0030060 L-malate dehydrogenase activity IEA
 molecular_functionGO:0051287 NAD binding IEA


Pathways (from Reactome)
Pathway description
Serine biosynthesis


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 HP:0000007 Autosomal recessive inheritance "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)." [HPO:curators]
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 HP:0000028 Cryptorchidism "Absence of one or both testes from the scrotum owing to failure of the testis or testes to descend through the inguinal canal to the testis." [HPO:curators]
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 HP:0000062 Ambiguous genitalia 
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 HP:0000104 Renal agenesis 
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 HP:0000135 Hypogonadism "Reduced function of the gonads (testes in males or ovaries in females)." [HPO:curators]
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 HP:0000136 Bifid uterus "A uterus that is divided into two lateral horns as a result of imperfect fusion of the paramesonephric ducts." [HPO:curators]
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 HP:0000175 Cleft palate "Cleft palate is a developmental defect of the `palate` (FMA:54549) resulting from a failure of fusion of the palatine processes." [HPO:curators]
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 HP:0000176 Submucous cleft palate "A cleft palate that is covered by the mucous membrane of the roof of the mouth, which can make the cleft more difficult to observe upon physical examination. Soft-palate submucous clefts are characterized by a midline deficiency or lack of muscle tissue. Hard-palate submucous clefts are characterized by bony defects in the midline of the bony palate. It may be possible to detect a submucous cleft palate upon palpation as a notch in the bony palate." [HPO:curators, pmid:19779505]
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 HP:0000179 Prominent lower lip "Increased thickness of the lower lip, leading to a prominent appearance of the lower lip." [HPO:curators]
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 HP:0000193 Bifid uvula "A split or cleft uvula." [HPO:curators]
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 HP:0000204 Cleft lip "A gap in the `upper lip` (FMA:59817). This is a congenital defect resulting from nonfusion of tissues of the lip during embryonal development." [HPO:probinson]
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 HP:0000211 Trismus "Limitation in the ability to open the mouth." [HPO:curators]
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 HP:0000232 Everted lower lip 
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 HP:0000252 Microcephaly "Microcephaly is a neurodevelopmental disorder in which the circumference of the head is more than two standard deviations smaller than the age- and gender-dependent norm." [HPO:curators]
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 HP:0000269 Prominent occiput 
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 HP:0000278 Retrognathia 
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 HP:0000288 Abnormality of the philtrum "An abnormality of the `philtrum` (FMA:59819)." [HPO:probinson]
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 HP:0000316 Hypertelorism 
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 HP:0000340 Sloping forehead "A form of the forehead that slopes from top to bottom in an anterior direction." [HPO:curators]
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 HP:0000347 Mandibular hypoplasia "Underdevelopment of the mandible." [HPO:curators]
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 HP:0000400 Large ears 
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 HP:0000457 Flat nose 
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 HP:0000470 Short neck 
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 HP:0000499 Abnormality of the eyelashes "An abnormality of the `eyelashes` (FMA:53669)." [HPO:probinson]
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 HP:0000518 Cataract "A cataract is an opacity or clouding that develops in the crystalline `lens` (FMA:58241) of the eye or in its `capsule` (FMA:58881)." [HPO:probinson]
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 HP:0000519 Congenital cataract "A congenital `cataract` (HP:0000518)." [HPO:probinson]
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 HP:0000520 Proptosis 
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 HP:0000561 Absent eyelashes "Lack of eyelashes." [HPO:curators]
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 HP:0000568 Microphthalmos "A developmental anomaly characterized by abnormal smallness of one or both eyes." [HPO:curators]
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 HP:0000614 Abnormality of the lacrimal duct 
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 HP:0000639 Nystagmus "Rhythmic, involuntary oscillations of one or both eyes related to abnormality in fixation, conjugate gaze, or vestibular mechanisms." [HPO:curators]
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 HP:0000938 Osteopenia "Osteopenia refers to a reduction in bone mineral density (BMD) below normal peak BMD but not low enough to be classified as osteoporosis. According to the WHO, osteopenia is characterized by a value of BMD more than 1 standard deviation below the young adult mean, but less than 2 standard deviations below this value." [HPO:curators]
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 HP:0000939 Osteoporosis "Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO, osteoporosis is characterized by a value of BMD 2.5 standard deviations or more below the young adult mean." [HPO:curators]
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 HP:0001059 Pterygia "Pterygia are winglike triangular membranes occurring in the neck, eyes, knees, elbows, ankles or digits." [HPO:curators]
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 HP:0001176 Large hands 
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 HP:0001181 Adducted thumbs 
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 HP:0001196 Short umbilical cord 
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 HP:0001249 Mental retardation 
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 HP:0001250 Seizures "Seizures are an intermittent `abnormality of the central nervous system` (FMA:HP:0002011) due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements." [HPO:probinson]
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 HP:0001274 Agenesis of corpus callosum "Absence of the corpus callosum as a result of the failure of the corpus callosum to develop, which can be the result of a failure in any one of the multiple steps of callosal development including cellular proliferation and migration, axonal growth or glial patterning at the midline." [HPO:curators]
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 HP:0001302 Pachygyria "A congenital abnormality of the cerebral hemisphere chacterized by unusually thick gyrations (convolutions) of the cerebral cortex." [HPO:curators]
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 HP:0001305 Dandy-Walker malformation "A congenital brain malformation typically characterized by incomplete formation of the cerebellar vermis, dilation of the fourth ventricle, and enlargement of the posterior fossa. In layman s terms, Dandy Walker malformation is a cyst in the cerebellum (typically symmetrical) that is involved with the fourth ventricle. This may interfere with the body s ability to drain cerebrospinal fluid from the brain, resulting in hydrocephalus. Dandy Walker cysts are formed during early embryonic development, while the brain forms. The cyst in the cerebellum typically has several blood vessels running through it connecting to the brain, thereby prohibiting surgical removal." [HPO:curators]
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 HP:0001321 Cerebellar hypoplasia 
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 HP:0001331 Absent septum pellucidum "Absence of the septum pellucidum." [HPO:curators]
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 HP:0001339 Lissencephaly "A congenital absence of the convolutions of the cerebral cortex and a poorly formed sylvian fissure." [HPO:curators]
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 HP:0001460 Aplasia/Hypoplasia involving the musculature "Absence or underdevelopment of the musculature." [HPO:curators]
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 HP:0001510 Growth retardation 
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 HP:0001511 Intrauterine growth retardation 
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 HP:0001558 Decreased fetal movement "An abnormal reduction in quantity or strength of fetal movements." [HPO:curators]
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 HP:0001561 Polyhydramnios 
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 HP:0001629 Ventricular septal defect "A hole between the two bottom chambers (ventricles) of the heart. The defect is centered around the most superior aspect of the ventricular septum." [HPO:curators]
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 HP:0001643 Patent ductus arteriosus 
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 HP:0001655 Patent foramen ovale 
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 HP:0001669 Transposition of the great vessels 
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 HP:0001769 Broad feet "Increased width of the feet." [HPO:curators]
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 HP:0001770 Toe syndactyly "Webbing or fusion of the toes, involving soft parts only or including bone structure. Bony fusions are revered to as "bony" Syndactyly if the fusion occurs in a radio-ulnar axis. Fusions of bones of the toes in a proximo-distal axis are refered to as "Symphalangism"." [HPO:curators]
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 HP:0001838 Vertical talus 
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 HP:0001848 Calcaneovalgus deformities 
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 HP:0001873 Thrombocytopenia 
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 HP:0001889 Megaloblastic anemia 
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 HP:0002089 Pulmonary hypoplasia 
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 HP:0002126 Polymicrogyria "A congenital abnormality of the cerebral hemisphere characterized by an excessive number of small gyri (convolutions) on the surface of the brain." [HPO:curators]
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 HP:0002179 Opisthotonus 
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 HP:0002190 Choroid plexus cyst 
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 HP:0002324 Hydranencephaly 
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 HP:0002414 Spina bifida "Incomplete closure of the embryonic neural tube, whereby some vertebral arches remain unfused and open." [HPO:curators]
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 HP:0002510 Spastic tetraplegia "Spastic paralysis affecting all four limbs." [HPO:curators]
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 HP:0002514 Cerebral calcification "The presence of calcification within brain structures." [HPO:curators]
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 HP:0002521 Hypsarrhythmia "Hypsarrhythmia is abnormal interictal high amplitude waves and a background of irregular spikes demonstrated by electroencephalography (EEG)." [HPO:curators]
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 HP:0002650 Scoliosis "The presence of an abnormal lateral curvature of the spine." [HPO:curators]
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 HP:0002748 Rickets 
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 HP:0002749 Osteomalacia "Osteomalacia is a general term for bone weakness owing to a defect in mineralization of the protein framework known as osteoid. This defective mineralization is mainly caused by lack in vitamin D. Osteomalacia in children is known as rickets." [HPO:curators]
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 HP:0002804 Arthrogryposis multiplex congenita 
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 HP:0002983 Micromelia 
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 HP:0003202 Amyotrophy "The presence of muscular atrophy (which is also known as amyotrophy)." [HPO:curators]
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 HP:0003241 Genital hypoplasia 
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 HP:0003394 Muscle cramps 
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 HP:0003560 Muscular dystrophy "The term dystrophy means abnormal growth. However, muscular dystrophy is used to describe primary myopathies with a genetic basis and a progressive course characterized by progressive skeletal muscle weakness, defects in muscle proteins, and the apoptosis of muscle cells." [HPO:curators]
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 HP:0003826 Stillborn or neonatal death 
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 HP:0006101 Finger syndactyly "Webbing or fusion of the fingers, involving soft parts only or including bone structure. Bony fusions are revered to as "bony" Syndactyly if the fusion occurs in a radio-ulnar axis. Fusions of bones of the fingers in a proximo-distal axis are refered to as "Symphalangism"." [HPO:curators]
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 HP:0006266 Small or abnormal placenta 
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 HP:0007227 Brain macrogyria and polymicrogyria 
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 HP:0007266 Dysmyelination of the brain 
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 HP:0007430 Generalized edema "Generalized abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body." [HPO:curators]
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 HP:0007525 Yellow subcutaneous tissue covered by thin, scaly skin 
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 HP:0008064 Ichthyosiform abnormality of the skin 
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 HP:0008734 Decreased testicular size 
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 HP:0009466 Radial deviation of fingers 
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 HP:0009473 Joint contractures involving the joints of the hand 
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 HP:0009826 Hypoplasia involving bones of the extremities 
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 HP:0011224 Ablepharon "Absent `eyelids` (FMA:75178)." [pmid:19125427]
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 HP:0011451 Congenital microcephaly "Microcephaly (HP:0000252) that is present already at the time of birth." [HPO:probinson]
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 HP:0012385 Camptodactyly "The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers or toes cannot be extended to 180 degrees by either active or passive extension." [HPO:probinson]
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 HP:0012471 Thick vermilion border "Increased width of the "skin of vermilion border region of upper lip" (FMA:312645)." [HPO:probinson]
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 HP:0030084 Clinodactyly "An angulation of a digit at an interphalangeal joint in the plane of the palm (finger) or sole (toe)." [pmid:16252026]
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 HP:0030680 Abnormality of cardiovascular system morphology "Any structural anomaly of the heart and great vessels." []
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 HP:0100679 Lack of skin elasticity 
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSG00000092621 PHGDH / O43175 / phosphoglycerate dehydrogenase  / complex






 

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