MCID: PHS021
MIFTS: 28

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 53 12 24 71 28 13 69
Phgdh Deficiency 53 12 24 71 14
3-Phosphoglycerate Dehydrogenase Deficiency 24 69
Phgdhd 53 71
3-Phosphoglycerate Dehydrogenase Deficiency, Infantile/juvenile Form 55
3-Phosphoglycerate Dehydrogenase Deficiency 36
Phosphoglycerate Dehydrogenase 13
3-Pgdh Deficiency 24

Characteristics:

Orphanet epidemiological data:

55

OMIM:

53
Inheritance:
autosomal recessive


HPO:

31
phosphoglycerate dehydrogenase deficiency:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Phosphoglycerate Dehydrogenase Deficiency

Genetics Home Reference : 24 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 seizures, nystagmus and intellectual disability. An important gene associated with Phosphoglycerate Dehydrogenase Deficiency is PHGDH (Phosphoglycerate Dehydrogenase), and among its related pathways/superpathways is Glycine, serine and threonine metabolism. Affiliated tissues include testes.

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

OMIM : 53 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)

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.

Wikipedia : 72 In enzymology, D-3-phosphoglycerate dehydrogenase (PHGDH) (EC 1.1.1.95) is an enzyme that primarily... more...

Related Diseases for Phosphoglycerate Dehydrogenase Deficiency

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

(show all 12)
# Related Disease Score Top Affiliating Genes
1 neu-laxova syndrome 1 11.2
2 pancreatic ductal adenocarcinoma 10.2
3 hepatosplenic t-cell lymphoma 10.2
4 cervicitis 10.0
5 west syndrome 10.0
6 microcephaly 9.9
7 epilepsy 9.9
8 schizophrenia 9.8
9 cervical cancer 9.8
10 gastric cancer 9.8
11 squamous cell carcinoma 9.8
12 adenocarcinoma 9.8

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:

53
Neurologic Central Nervous System:
seizures
hypertonia
mental retardation
dysmyelination
spastic quadriplegia
more
Hematology:
thrombocytopenia
megaloblastic anemia

Skeletal Hands:
adducted thumbs

Head And Neck Head:
microcephaly, congenital

Head And Neck Eyes:
nystagmus
cataracts, congenital

Growth Other:
growth retardation

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:

31 (show all 13)
# Description HPO Frequency HPO Source Accession
1 seizures 31 HP:0001250
2 nystagmus 31 HP:0000639
3 intellectual disability 31 HP:0001249
4 spastic tetraplegia 31 HP:0002510
5 growth delay 31 HP:0001510
6 thrombocytopenia 31 HP:0001873
7 decreased testicular size 31 HP:0008734
8 adducted thumb 31 HP:0001181
9 hypsarrhythmia 31 HP:0002521
10 congenital cataract 31 HP:0000519
11 megaloblastic anemia 31 HP:0001889
12 congenital microcephaly 31 HP:0011451
13 cerebral dysmyelination 31 HP:0007266

UMLS symptoms related to Phosphoglycerate Dehydrogenase Deficiency:


seizures

Drugs & Therapeutics for Phosphoglycerate Dehydrogenase Deficiency

Search Clinical Trials , NIH Clinical Center for Phosphoglycerate Dehydrogenase Deficiency

Genetic Tests for Phosphoglycerate Dehydrogenase Deficiency

Genetic tests related to Phosphoglycerate Dehydrogenase Deficiency:

# Genetic test Affiliating Genes
1 Phosphoglycerate Dehydrogenase Deficiency 28 PHGDH

Anatomical Context for Phosphoglycerate Dehydrogenase Deficiency

MalaCards organs/tissues related to Phosphoglycerate Dehydrogenase Deficiency:

38
Testes

Publications for Phosphoglycerate Dehydrogenase Deficiency

Articles related to Phosphoglycerate Dehydrogenase Deficiency:

# 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
# 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
# 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

Pathways related to Phosphoglycerate Dehydrogenase Deficiency according to KEGG:

36
# Name Kegg Source Accession
1 Glycine, serine and threonine metabolism hsa00260

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
27 GO
28 GTR
29 HGMD
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 MedGen
41 MeSH
42 MESH via Orphanet
43 MGI
45 NCI
46 NCIt
47 NDF-RT
50 NINDS
51 Novoseek
53 OMIM
54 OMIM via Orphanet
58 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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