MCID: PHS021
MIFTS: 31

Phosphoglycerate Dehydrogenase Deficiency

Categories: Genetic diseases, Neuronal diseases, Metabolic diseases, Rare diseases

Aliases & Classifications for Phosphoglycerate Dehydrogenase Deficiency

MalaCards integrated aliases for Phosphoglycerate Dehydrogenase Deficiency:

Name: Phosphoglycerate Dehydrogenase Deficiency 54 12 24 25 71 29 13 69
Phgdh Deficiency 12 24 25 71 14
3-Phosphoglycerate Dehydrogenase Deficiency 25 69
3-Phosphoglycerate Dehydrogenase Deficiency, Infantile/juvenile Form 56
Phosphoglycerate Dehydrogenase 13
3-Pgdh Deficiency 25
Phgdhd 71

Characteristics:

Orphanet epidemiological data:

56

OMIM:

54
Inheritance:
autosomal recessive


HPO:

32
phosphoglycerate dehydrogenase deficiency:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Phosphoglycerate Dehydrogenase Deficiency

Genetics Home Reference : 25 Phosphoglycerate dehydrogenase deficiency is a condition characterized by an unusually small head size (microcephaly); impaired development of physical reactions, movements, and speech (psychomotor retardation); and recurrent seizures (epilepsy). Different types of phosphoglycerate dehydrogenase deficiency have been described; they are distinguished by their severity and the age at which symptoms first begin. Most affected individuals have the infantile form, which is the most severe form, and are affected from infancy. Symptoms of the juvenile and adult types appear later in life; these types are very rare.

MalaCards based summary : Phosphoglycerate Dehydrogenase Deficiency, also known as phgdh deficiency, is related to neu-laxova syndrome 1 and pancreatic ductal adenocarcinoma, and has symptoms including congenital cataract, nystagmus and seizures. An important gene associated with Phosphoglycerate Dehydrogenase Deficiency is PHGDH (Phosphoglycerate Dehydrogenase). The drug Pharmaceutical Solutions has been mentioned in the context of this disorder. Affiliated tissues include testes.

UniProtKB/Swiss-Prot : 71 Phosphoglycerate dehydrogenase deficiency: An autosomal recessive inborn error of L-serine biosynthesis, clinically characterized by congenital microcephaly, psychomotor retardation, and seizures.

OMIM : 54
Phosphoglycerate dehydrogenase deficiency is an autosomal recessive inborn error of L-serine biosynthesis that is characterized by congenital microcephaly, psychomotor retardation, and seizures (summary by Jaeken et al., 1996). (601815)

Disease Ontology : 12 A serine deficiency that has material basis in deficiency of phosphoglycerate dehydrogenase which results in a disruption of L-serine biosynthesis.

Wikipedia : 72 2G76... more...

Related Diseases for Phosphoglycerate Dehydrogenase Deficiency

Diseases related to Phosphoglycerate Dehydrogenase Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

id Related Disease Score Top Affiliating Genes
1 neu-laxova syndrome 1 11.1
2 pancreatic ductal adenocarcinoma 10.1
3 hepatosplenic t-cell lymphoma 10.1
4 cervicitis 9.9
5 microcephaly 9.8
6 epilepsy 9.8
7 primary microcephaly 9.8
8 schizophrenia 9.7

Graphical network of the top 20 diseases related to Phosphoglycerate Dehydrogenase Deficiency:



Diseases related to Phosphoglycerate Dehydrogenase Deficiency

Symptoms & Phenotypes for Phosphoglycerate Dehydrogenase Deficiency

Symptoms via clinical synopsis from OMIM:

54

Neurologic- Central Nervous System:
mental retardation
seizures
hypertonia
spastic quadriplegia
dysmyelination
more
Growth- Other:
growth retardation

Head And Neck- Head:
microcephaly, congenital

Skeletal- Hands:
adducted thumbs

Head And Neck- Eyes:
nystagmus
cataracts, congenital

Hematology:
megaloblastic anemia
thrombocytopenia

Genitourinary- Internal Genitalia Male:
small testes

Laboratory- Abnormalities:
decrease plasma serine (fasting)
decreased csf serine
decreased phgdh activity (fibroblasts)
normal-to-decreased plasma glycine (fasting)
decreased csf glycine


Clinical features from OMIM:

601815

Human phenotypes related to Phosphoglycerate Dehydrogenase Deficiency:

32 (show all 13)
id Description HPO Frequency HPO Source Accession
1 congenital cataract 32 HP:0000519
2 nystagmus 32 HP:0000639
3 seizures 32 HP:0001250
4 megaloblastic anemia 32 HP:0001889
5 thrombocytopenia 32 HP:0001873
6 hypsarrhythmia 32 HP:0002521
7 intellectual disability 32 HP:0001249
8 spastic tetraplegia 32 HP:0002510
9 decreased testicular size 32 HP:0008734
10 growth delay 32 HP:0001510
11 congenital microcephaly 32 HP:0011451
12 adducted thumb 32 HP:0001181
13 cerebral dysmyelination 32 HP:0007266

UMLS symptoms related to Phosphoglycerate Dehydrogenase Deficiency:


seizures

Drugs & Therapeutics for Phosphoglycerate Dehydrogenase Deficiency

Drugs for Phosphoglycerate Dehydrogenase Deficiency (from DrugBank, HMDB, Dgidb, PharmGKB, IUPHAR, NovoSeek, BitterDB):


id Name Status Phase Clinical Trials Cas Number PubChem Id
1 Pharmaceutical Solutions

Interventional clinical trials:


id Name Status NCT ID Phase Drugs
1 Fat and Sugar Metabolism During Exercise in Patients With Metabolic Myopathy Recruiting NCT02635269

Search NIH Clinical Center for Phosphoglycerate Dehydrogenase Deficiency

Genetic Tests for Phosphoglycerate Dehydrogenase Deficiency

Genetic tests related to Phosphoglycerate Dehydrogenase Deficiency:

id Genetic test Affiliating Genes
1 Phosphoglycerate Dehydrogenase Deficiency 29 24 PHGDH

Anatomical Context for Phosphoglycerate Dehydrogenase Deficiency

MalaCards organs/tissues related to Phosphoglycerate Dehydrogenase Deficiency:

39
Testes

Publications for Phosphoglycerate Dehydrogenase Deficiency

Articles related to Phosphoglycerate Dehydrogenase Deficiency:

id Title Authors Year
1
Infantile Serine Biosynthesis Defect Due to Phosphoglycerate Dehydrogenase Deficiency: Variability in Phenotype and Treatment Response, Novel Mutations, and Diagnostic Challenges. ( 28135894 )
2017

Variations for Phosphoglycerate Dehydrogenase Deficiency

UniProtKB/Swiss-Prot genetic disease variations for Phosphoglycerate Dehydrogenase Deficiency:

71
id Symbol AA change Variation ID SNP ID
1 PHGDH p.Val425Met VAR_013461 rs121907988
2 PHGDH p.Arg135Trp VAR_059026 rs267606949
3 PHGDH p.Val261Met VAR_059027 rs267606947
4 PHGDH p.Ala373Thr VAR_059028
5 PHGDH p.Gly377Ser VAR_059029 rs267606948
6 PHGDH p.Val490Met VAR_059030 rs121907987

ClinVar genetic disease variations for Phosphoglycerate Dehydrogenase Deficiency:

6
id Gene Variation Type Significance SNP ID Assembly Location
1 PHGDH NM_006623.3(PHGDH): c.1468G> A (p.Val490Met) single nucleotide variant Pathogenic rs121907987 GRCh37 Chromosome 1, 120286529: 120286529
2 PHGDH NM_006623.3(PHGDH): c.1273G> A (p.Val425Met) single nucleotide variant Pathogenic rs121907988 GRCh37 Chromosome 1, 120285493: 120285493
3 PHGDH NM_006623.3(PHGDH): c.714delG (p.Ile239Serfs) deletion Pathogenic rs730882181 GRCh37 Chromosome 1, 120277988: 120277988
4 PHGDH NM_006623.3(PHGDH): c.403C> T (p.Arg135Trp) single nucleotide variant Pathogenic rs267606949 GRCh37 Chromosome 1, 120269520: 120269520
5 PHGDH NM_006623.3(PHGDH): c.1129G> A (p.Gly377Ser) single nucleotide variant Pathogenic rs267606948 GRCh37 Chromosome 1, 120284440: 120284440
6 PHGDH NM_006623.3(PHGDH): c.781G> A (p.Val261Met) single nucleotide variant Pathogenic rs267606947 GRCh37 Chromosome 1, 120278055: 120278055

Expression for Phosphoglycerate Dehydrogenase Deficiency

Search GEO for disease gene expression data for Phosphoglycerate Dehydrogenase Deficiency.

Pathways for Phosphoglycerate Dehydrogenase Deficiency

GO Terms for Phosphoglycerate Dehydrogenase Deficiency

Sources for Phosphoglycerate Dehydrogenase Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
16 ExPASy
18 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 MedGen
42 MeSH
43 MESH via Orphanet
44 MGI
46 NCI
47 NCIt
48 NDF-RT
51 NINDS
52 Novoseek
54 OMIM
55 OMIM via Orphanet
59 PubMed
60 QIAGEN
65 SNOMED-CT via HPO
66 SNOMED-CT via Orphanet
67 TGDB
68 Tocris
69 UMLS
70 UMLS via Orphanet
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