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 57 12 25 75 29 13 6 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 Glucose / Energy Metabolism. Affiliated tissues include testes, 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

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

(show all 11)
# Related Disease Score Top Affiliating Genes
1 neu-laxova syndrome 1 30.2 LOC105378936 PHGDH
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

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

GenitourinaryInternal GenitaliaMale:
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

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

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:

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 74)
# 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 Pathogenic rs267606949 GRCh37 Chromosome 1, 120269520: 120269520
8 PHGDH NM_006623.3(PHGDH): c.403C> T (p.Arg135Trp) single nucleotide variant Pathogenic 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 Pathogenic rs267606947 GRCh37 Chromosome 1, 120278055: 120278055
12 PHGDH NM_006623.3(PHGDH): c.781G> A (p.Val261Met) single nucleotide variant Pathogenic rs267606947 GRCh38 Chromosome 1, 119735432: 119735432
13 PHGDH NM_006623.3(PHGDH): c.-207G> A single nucleotide variant Uncertain significance rs150128831 GRCh38 Chromosome 1, 119711816: 119711816
14 PHGDH NM_006623.3(PHGDH): c.-207G> A single nucleotide variant Uncertain significance rs150128831 GRCh37 Chromosome 1, 120254439: 120254439
15 PHGDH NM_006623.3(PHGDH): c.-101G> C single nucleotide variant Benign rs562038 GRCh38 Chromosome 1, 119711922: 119711922
16 PHGDH NM_006623.3(PHGDH): c.-101G> C single nucleotide variant Benign rs562038 GRCh37 Chromosome 1, 120254545: 120254545
17 PHGDH NM_006623.3(PHGDH): c.139-13T> C single nucleotide variant Likely benign rs894078 GRCh37 Chromosome 1, 120263780: 120263780
18 PHGDH NM_006623.3(PHGDH): c.139-13T> C single nucleotide variant Likely benign rs894078 GRCh38 Chromosome 1, 119721157: 119721157
19 PHGDH NM_006623.3(PHGDH): c.390C> T (p.Asp130=) single nucleotide variant Uncertain significance rs148078511 GRCh37 Chromosome 1, 120269507: 120269507
20 PHGDH NM_006623.3(PHGDH): c.390C> T (p.Asp130=) single nucleotide variant Uncertain significance rs148078511 GRCh38 Chromosome 1, 119726884: 119726884
21 PHGDH NM_006623.3(PHGDH): c.624T> C (p.Pro208=) single nucleotide variant Conflicting interpretations of pathogenicity rs77401816 GRCh37 Chromosome 1, 120277370: 120277370
22 PHGDH NM_006623.3(PHGDH): c.624T> C (p.Pro208=) single nucleotide variant Conflicting interpretations of pathogenicity rs77401816 GRCh38 Chromosome 1, 119734747: 119734747
23 PHGDH NM_006623.3(PHGDH): c.834C> A (p.Val278=) single nucleotide variant Uncertain significance rs147866831 GRCh37 Chromosome 1, 120279778: 120279778
24 PHGDH NM_006623.3(PHGDH): c.834C> A (p.Val278=) single nucleotide variant Uncertain significance rs147866831 GRCh38 Chromosome 1, 119737155: 119737155
25 PHGDH NM_006623.3(PHGDH): c.916A> G (p.Met306Val) single nucleotide variant Uncertain significance rs587648058 GRCh37 Chromosome 1, 120279860: 120279860
26 PHGDH NM_006623.3(PHGDH): c.916A> G (p.Met306Val) single nucleotide variant Uncertain significance rs587648058 GRCh38 Chromosome 1, 119737237: 119737237
27 HMGCS2; PHGDH NM_005518.3(HMGCS2): c.*165C> T single nucleotide variant Likely benign rs138575225 GRCh37 Chromosome 1, 120291305: 120291305
28 HMGCS2; PHGDH NM_005518.3(HMGCS2): c.*165C> T single nucleotide variant Likely benign rs138575225 GRCh38 Chromosome 1, 119748682: 119748682
29 PHGDH NM_006623.3(PHGDH): c.-11C> T single nucleotide variant Uncertain significance rs886045203 GRCh38 Chromosome 1, 119712012: 119712012
30 PHGDH NM_006623.3(PHGDH): c.-222G> A single nucleotide variant Uncertain significance rs60544490 GRCh38 Chromosome 1, 119711801: 119711801
31 PHGDH NM_006623.3(PHGDH): c.-222G> A single nucleotide variant Uncertain significance rs60544490 GRCh37 Chromosome 1, 120254424: 120254424
32 PHGDH NM_006623.3(PHGDH): c.-11C> T single nucleotide variant Uncertain significance rs886045203 GRCh37 Chromosome 1, 120254635: 120254635
33 PHGDH NM_006623.3(PHGDH): c.138G> A (p.Gln46=) single nucleotide variant Uncertain significance rs143217390 GRCh38 Chromosome 1, 119712160: 119712160
34 PHGDH NM_006623.3(PHGDH): c.138G> A (p.Gln46=) single nucleotide variant Uncertain significance rs143217390 GRCh37 Chromosome 1, 120254783: 120254783
35 PHGDH NM_006623.3(PHGDH): c.1078+10G> T single nucleotide variant Uncertain significance rs374994783 GRCh37 Chromosome 1, 120283151: 120283151
36 PHGDH NM_006623.3(PHGDH): c.1078+10G> T single nucleotide variant Uncertain significance rs374994783 GRCh38 Chromosome 1, 119740528: 119740528
37 PHGDH NM_006623.3(PHGDH): c.1326G> A (p.Thr442=) single nucleotide variant Benign rs543703 GRCh37 Chromosome 1, 120285546: 120285546
38 PHGDH NM_006623.3(PHGDH): c.1326G> A (p.Thr442=) single nucleotide variant Benign rs543703 GRCh38 Chromosome 1, 119742923: 119742923
39 PHGDH NM_006623.3(PHGDH): c.-183G> A single nucleotide variant Uncertain significance rs886045202 GRCh38 Chromosome 1, 119711840: 119711840
40 PHGDH NM_006623.3(PHGDH): c.-183G> A single nucleotide variant Uncertain significance rs886045202 GRCh37 Chromosome 1, 120254463: 120254463
41 PHGDH NM_006623.3(PHGDH): c.381G> A (p.Ser127=) single nucleotide variant Uncertain significance rs886045205 GRCh37 Chromosome 1, 120269498: 120269498
42 PHGDH NM_006623.3(PHGDH): c.381G> A (p.Ser127=) single nucleotide variant Uncertain significance rs886045205 GRCh38 Chromosome 1, 119726875: 119726875
43 PHGDH NM_006623.3(PHGDH): c.543G> A (p.Glu181=) single nucleotide variant Uncertain significance rs886045206 GRCh37 Chromosome 1, 120277289: 120277289
44 PHGDH NM_006623.3(PHGDH): c.543G> A (p.Glu181=) single nucleotide variant Uncertain significance rs886045206 GRCh38 Chromosome 1, 119734666: 119734666
45 PHGDH NM_006623.3(PHGDH): c.1158G> A (p.Ala386=) single nucleotide variant Uncertain significance rs144484007 GRCh37 Chromosome 1, 120284469: 120284469
46 PHGDH NM_006623.3(PHGDH): c.1158G> A (p.Ala386=) single nucleotide variant Uncertain significance rs144484007 GRCh38 Chromosome 1, 119741846: 119741846
47 PHGDH NM_006623.3(PHGDH): c.1285G> C (p.Gly429Arg) single nucleotide variant Uncertain significance rs145854744 GRCh37 Chromosome 1, 120285505: 120285505
48 PHGDH NM_006623.3(PHGDH): c.1285G> C (p.Gly429Arg) single nucleotide variant Uncertain significance rs145854744 GRCh38 Chromosome 1, 119742882: 119742882
49 HMGCS2; PHGDH NM_005518.3(HMGCS2): c.*332A> C single nucleotide variant Likely benign rs56828380 GRCh37 Chromosome 1, 120291138: 120291138
50 HMGCS2; PHGDH NM_005518.3(HMGCS2): c.*332A> C single nucleotide variant Likely benign rs56828380 GRCh38 Chromosome 1, 119748515: 119748515

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

Pathways related to Phosphoglycerate Dehydrogenase Deficiency according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 11.11 HMGCS2 PHGDH

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 metabolic process GO:0008152 8.62 HMGCS2 PHGDH

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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