PHGDHD
MCID: PHS021
MIFTS: 44

Phosphoglycerate Dehydrogenase Deficiency (PHGDHD)

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

Aliases & Classifications for Phosphoglycerate Dehydrogenase Deficiency

MalaCards integrated aliases for Phosphoglycerate Dehydrogenase Deficiency:

Name: Phosphoglycerate Dehydrogenase Deficiency 57 12 25 75 29 13 6 44 73
Phgdh Deficiency 57 12 25 75 15
3-Phosphoglycerate Dehydrogenase Deficiency 25 73
Phgdhd 57 75
3-Phosphoglycerate Dehydrogenase Deficiency, Infantile/juvenile Form 59
3-Phosphoglycerate Dehydrogenase Deficiency 37
Deficiency, Phosphoglycerate Dehydrogenase 40
Phosphoglycerate Dehydrogenase 13
3-Pgdh Deficiency 25

Characteristics:

Orphanet epidemiological data:

59

OMIM:

57
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 seizures An important gene associated with Phosphoglycerate Dehydrogenase Deficiency is PHGDH (Phosphoglycerate Dehydrogenase), and among its related pathways/superpathways are Glycine, serine and threonine metabolism and Wnt Signaling Pathway and Pluripotency. Affiliated tissues include testes, brain and t cells, and related phenotypes are nystagmus and intellectual disability

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 : 57 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 : 75 Phosphoglycerate dehydrogenase deficiency: An autosomal recessive inborn error of L-serine biosynthesis, clinically characterized by congenital microcephaly, psychomotor retardation, and seizures.

Wikipedia : 76 In enzymology, D-3-phosphoglycerate dehydrogenase (PHGDH) (EC 1.1.1.95) is an enzyme that primarily... more...

Related Diseases for Phosphoglycerate Dehydrogenase Deficiency

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:

57
Head And Neck Eyes:
nystagmus
cataracts, congenital

Hematology:
thrombocytopenia
megaloblastic anemia

Skeletal Hands:
adducted thumbs

Head And Neck Head:
microcephaly, congenital

Neurologic Central Nervous System:
seizures
hypertonia
mental retardation
dysmyelination
spastic quadriplegia
more
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:

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

Cochrane evidence based reviews: phosphoglycerate dehydrogenase deficiency

Genetic Tests for Phosphoglycerate Dehydrogenase Deficiency

Genetic tests related to Phosphoglycerate Dehydrogenase Deficiency:

# Genetic test Affiliating Genes
1 Phosphoglycerate Dehydrogenase Deficiency 29 PHGDH

Anatomical Context for Phosphoglycerate Dehydrogenase Deficiency

MalaCards organs/tissues related to Phosphoglycerate Dehydrogenase Deficiency:

41
Testes, Brain, T Cells

Publications for Phosphoglycerate Dehydrogenase Deficiency

Articles related to Phosphoglycerate Dehydrogenase Deficiency:

(show all 16)
# Title Authors Year
1
Reduction of stratum corneum ceramides in Neu-Laxova syndrome caused by phosphoglycerate dehydrogenase deficiency. ( 30348640 )
2018
2
Infantile Serine Biosynthesis Defect Due to Phosphoglycerate Dehydrogenase Deficiency: Variability in Phenotype and Treatment Response, Novel Mutations, and Diagnostic Challenges. ( 28135894 )
2017
3
3-Phosphoglycerate dehydrogenase deficiency: description of two new cases in Tunisia and review of the literature. ( 23564319 )
2013
4
Expanding the clinical spectrum of 3-phosphoglycerate dehydrogenase deficiency. ( 21113737 )
2011
5
3-phosphoglycerate dehydrogenase deficiency: a case report of a treatable cause of seizures. ( 20196394 )
2009
6
Prenatal and early postnatal treatment in 3-phosphoglycerate-dehydrogenase deficiency. ( 15610810 )
2004
7
V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. ( 11751922 )
2002
8
Congenital microcephaly and seizures due to 3-phosphoglycerate dehydrogenase deficiency: outcome of treatment with amino acids. ( 12118526 )
2002
9
Phenotypic heterogeneity and adverse effects of serine treatment in 3-phosphoglycerate dehydrogenase deficiency: report on two siblings. ( 11571699 )
2001
10
Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency -- a neurometabolic disorder associated with reduced L- serine biosynthesis. ( 11055895 )
2000
11
3-phosphoglycerate dehydrogenase deficiency in a patient with West syndrome. ( 11034457 )
2000
12
Hypomyelination and reversible white matter attenuation in 3-phosphoglycerate dehydrogenase deficiency. ( 11508546 )
2000
13
Neurotransmitters in 3-phosphoglycerate dehydrogenase deficiency. ( 11131361 )
2000
14
Beneficial effects of L-serine and glycine in the management of seizures in 3-phosphoglycerate dehydrogenase deficiency. ( 9708551 )
1998
15
3-Phosphoglycerate dehydrogenase deficiency: an inborn error of serine biosynthesis. ( 8758134 )
1996
16
3-Phosphoglycerate dehydrogenase deficiency and 3-phosphoserine phosphatase deficiency: inborn errors of serine biosynthesis. ( 8739971 )
1996

Variations for Phosphoglycerate Dehydrogenase Deficiency

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

75
# 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 (show top 50) (show all 80)
# 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.1468G> A (p.Val490Met) single nucleotide variant Pathogenic rs121907987 GRCh38 Chromosome 1, 119743906: 119743906
3 PHGDH NM_006623.3(PHGDH): c.1273G> A (p.Val425Met) single nucleotide variant Pathogenic rs121907988 GRCh37 Chromosome 1, 120285493: 120285493
4 PHGDH NM_006623.3(PHGDH): c.1273G> A (p.Val425Met) single nucleotide variant Pathogenic rs121907988 GRCh38 Chromosome 1, 119742870: 119742870
5 PHGDH NM_006623.3(PHGDH): c.714delG (p.Ile239Serfs) deletion Pathogenic rs730882181 GRCh37 Chromosome 1, 120277988: 120277988
6 PHGDH NM_006623.3(PHGDH): c.714delG (p.Ile239Serfs) deletion Pathogenic rs730882181 GRCh38 Chromosome 1, 119735365: 119735365
7 PHGDH NM_006623.3(PHGDH): c.403C> T (p.Arg135Trp) single nucleotide variant Uncertain significance rs267606949 GRCh37 Chromosome 1, 120269520: 120269520
8 PHGDH NM_006623.3(PHGDH): c.403C> T (p.Arg135Trp) single nucleotide variant Uncertain significance rs267606949 GRCh38 Chromosome 1, 119726897: 119726897
9 PHGDH NM_006623.3(PHGDH): c.1129G> A (p.Gly377Ser) single nucleotide variant Pathogenic rs267606948 GRCh37 Chromosome 1, 120284440: 120284440
10 PHGDH NM_006623.3(PHGDH): c.1129G> A (p.Gly377Ser) single nucleotide variant Pathogenic rs267606948 GRCh38 Chromosome 1, 119741817: 119741817
11 PHGDH NM_006623.3(PHGDH): c.781G> A (p.Val261Met) single nucleotide variant Likely pathogenic rs267606947 GRCh37 Chromosome 1, 120278055: 120278055
12 PHGDH NM_006623.3(PHGDH): c.781G> A (p.Val261Met) single nucleotide variant Likely pathogenic rs267606947 GRCh38 Chromosome 1, 119735432: 119735432
13 PHGDH NM_006623.3(PHGDH): c.488G> A (p.Arg163Gln) single nucleotide variant Uncertain significance rs587777483 GRCh37 Chromosome 1, 120269703: 120269703
14 PHGDH NM_006623.3(PHGDH): c.488G> A (p.Arg163Gln) single nucleotide variant Uncertain significance rs587777483 GRCh38 Chromosome 1, 119727080: 119727080
15 PHGDH NM_006623.3(PHGDH): c.-207G> A single nucleotide variant Uncertain significance rs150128831 GRCh38 Chromosome 1, 119711816: 119711816
16 PHGDH NM_006623.3(PHGDH): c.-207G> A single nucleotide variant Uncertain significance rs150128831 GRCh37 Chromosome 1, 120254439: 120254439
17 PHGDH NM_006623.3(PHGDH): c.-101G> C single nucleotide variant Benign rs562038 GRCh38 Chromosome 1, 119711922: 119711922
18 PHGDH NM_006623.3(PHGDH): c.-101G> C single nucleotide variant Benign rs562038 GRCh37 Chromosome 1, 120254545: 120254545
19 PHGDH NM_006623.3(PHGDH): c.139-13T> C single nucleotide variant Likely benign rs894078 GRCh37 Chromosome 1, 120263780: 120263780
20 PHGDH NM_006623.3(PHGDH): c.139-13T> C single nucleotide variant Likely benign rs894078 GRCh38 Chromosome 1, 119721157: 119721157
21 PHGDH NM_006623.3(PHGDH): c.390C> T (p.Asp130=) single nucleotide variant Uncertain significance rs148078511 GRCh37 Chromosome 1, 120269507: 120269507
22 PHGDH NM_006623.3(PHGDH): c.390C> T (p.Asp130=) single nucleotide variant Uncertain significance rs148078511 GRCh38 Chromosome 1, 119726884: 119726884
23 PHGDH NM_006623.3(PHGDH): c.624T> C (p.Pro208=) single nucleotide variant Conflicting interpretations of pathogenicity rs77401816 GRCh37 Chromosome 1, 120277370: 120277370
24 PHGDH NM_006623.3(PHGDH): c.624T> C (p.Pro208=) single nucleotide variant Conflicting interpretations of pathogenicity rs77401816 GRCh38 Chromosome 1, 119734747: 119734747
25 PHGDH NM_006623.3(PHGDH): c.834C> A (p.Val278=) single nucleotide variant Uncertain significance rs147866831 GRCh37 Chromosome 1, 120279778: 120279778
26 PHGDH NM_006623.3(PHGDH): c.834C> A (p.Val278=) single nucleotide variant Uncertain significance rs147866831 GRCh38 Chromosome 1, 119737155: 119737155
27 PHGDH NM_006623.3(PHGDH): c.916A> G (p.Met306Val) single nucleotide variant Uncertain significance rs587648058 GRCh37 Chromosome 1, 120279860: 120279860
28 PHGDH NM_006623.3(PHGDH): c.916A> G (p.Met306Val) single nucleotide variant Uncertain significance rs587648058 GRCh38 Chromosome 1, 119737237: 119737237
29 HMGCS2; PHGDH NM_005518.3(HMGCS2): c.*165C> T single nucleotide variant Likely benign rs138575225 GRCh37 Chromosome 1, 120291305: 120291305
30 HMGCS2; PHGDH NM_005518.3(HMGCS2): c.*165C> T single nucleotide variant Likely benign rs138575225 GRCh38 Chromosome 1, 119748682: 119748682
31 PHGDH NM_006623.3(PHGDH): c.-222G> A single nucleotide variant Uncertain significance rs60544490 GRCh38 Chromosome 1, 119711801: 119711801
32 PHGDH NM_006623.3(PHGDH): c.-222G> A single nucleotide variant Uncertain significance rs60544490 GRCh37 Chromosome 1, 120254424: 120254424
33 PHGDH NM_006623.3(PHGDH): c.-11C> T single nucleotide variant Uncertain significance rs886045203 GRCh38 Chromosome 1, 119712012: 119712012
34 PHGDH NM_006623.3(PHGDH): c.-11C> T single nucleotide variant Uncertain significance rs886045203 GRCh37 Chromosome 1, 120254635: 120254635
35 PHGDH NM_006623.3(PHGDH): c.138G> A (p.Gln46=) single nucleotide variant Uncertain significance rs143217390 GRCh38 Chromosome 1, 119712160: 119712160
36 PHGDH NM_006623.3(PHGDH): c.138G> A (p.Gln46=) single nucleotide variant Uncertain significance rs143217390 GRCh37 Chromosome 1, 120254783: 120254783
37 PHGDH NM_006623.3(PHGDH): c.1078+10G> T single nucleotide variant Uncertain significance rs374994783 GRCh37 Chromosome 1, 120283151: 120283151
38 PHGDH NM_006623.3(PHGDH): c.1078+10G> T single nucleotide variant Uncertain significance rs374994783 GRCh38 Chromosome 1, 119740528: 119740528
39 PHGDH NM_006623.3(PHGDH): c.1326G> A (p.Thr442=) single nucleotide variant Benign rs543703 GRCh37 Chromosome 1, 120285546: 120285546
40 PHGDH NM_006623.3(PHGDH): c.1326G> A (p.Thr442=) single nucleotide variant Benign rs543703 GRCh38 Chromosome 1, 119742923: 119742923
41 PHGDH NM_006623.3(PHGDH): c.-183G> A single nucleotide variant Uncertain significance rs886045202 GRCh38 Chromosome 1, 119711840: 119711840
42 PHGDH NM_006623.3(PHGDH): c.-183G> A single nucleotide variant Uncertain significance rs886045202 GRCh37 Chromosome 1, 120254463: 120254463
43 PHGDH NM_006623.3(PHGDH): c.381G> A (p.Ser127=) single nucleotide variant Uncertain significance rs886045205 GRCh37 Chromosome 1, 120269498: 120269498
44 PHGDH NM_006623.3(PHGDH): c.381G> A (p.Ser127=) single nucleotide variant Uncertain significance rs886045205 GRCh38 Chromosome 1, 119726875: 119726875
45 PHGDH NM_006623.3(PHGDH): c.543G> A (p.Glu181=) single nucleotide variant Uncertain significance rs886045206 GRCh37 Chromosome 1, 120277289: 120277289
46 PHGDH NM_006623.3(PHGDH): c.543G> A (p.Glu181=) single nucleotide variant Uncertain significance rs886045206 GRCh38 Chromosome 1, 119734666: 119734666
47 PHGDH NM_006623.3(PHGDH): c.1158G> A (p.Ala386=) single nucleotide variant Uncertain significance rs144484007 GRCh37 Chromosome 1, 120284469: 120284469
48 PHGDH NM_006623.3(PHGDH): c.1158G> A (p.Ala386=) single nucleotide variant Uncertain significance rs144484007 GRCh38 Chromosome 1, 119741846: 119741846
49 PHGDH NM_006623.3(PHGDH): c.1285G> C (p.Gly429Arg) single nucleotide variant Uncertain significance rs145854744 GRCh37 Chromosome 1, 120285505: 120285505
50 PHGDH NM_006623.3(PHGDH): c.1285G> C (p.Gly429Arg) single nucleotide variant Uncertain significance rs145854744 GRCh38 Chromosome 1, 119742882: 119742882

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:

37
# Name Kegg Source Accession
1 Glycine, serine and threonine metabolism hsa00260

GO Terms for Phosphoglycerate Dehydrogenase Deficiency

Biological processes related to Phosphoglycerate Dehydrogenase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 regulation of gene expression GO:0010468 9.35 BMI1 NANOG PHGDH POU5F1 SOX2
2 somatic stem cell population maintenance GO:0035019 9.33 NANOG POU5F1 SOX2
3 neurogenesis GO:0022008 9.26 BHLHE22 PHGDH
4 endodermal cell fate specification GO:0001714 8.8 NANOG POU5F1 SOX2

Molecular functions related to Phosphoglycerate Dehydrogenase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 miRNA binding GO:0035198 8.62 POU5F1 SOX2

Sources for Phosphoglycerate Dehydrogenase Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 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 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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