PHGDHD
MCID: PHS021
MIFTS: 47

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 56 12 25 73 29 13 6 43 71
Phgdh Deficiency 56 12 25 73 15
3-Phosphoglycerate Dehydrogenase Deficiency 25 29 71
Phgdhd 56 73
3-Phosphoglycerate Dehydrogenase Deficiency, Infantile/juvenile Form 58
3-Phosphoglycerate Dehydrogenase Deficiency 36
Deficiency, Phosphoglycerate Dehydrogenase 39
Phgdh Deficiency, Infantile/juvenile Form 58
3-Pgdh Deficiency 25

Characteristics:

Orphanet epidemiological data:

58

OMIM:

56
Inheritance:
autosomal recessive


HPO:

31
phosphoglycerate dehydrogenase deficiency:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 58  
Rare neurological diseases
Inborn errors of metabolism


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. In phosphoglycerate dehydrogenase deficiency there is a progressive loss of brain cells leading to a loss of brain tissue (brain atrophy), specifically affecting the fatty tissue known as myelin that surrounds nerve cells (hypomyelination). Frequently, the tissue that connects the two halves of the brain (corpus callosum) is small and thin, and the fluid-filled cavities (ventricles) near the center of the brain are enlarged. Because development of the brain is disrupted, the head does not grow at the same rate as the body, so it appears that the head is getting smaller as the body grows (progressive microcephaly). Poor brain growth leads to an inability to achieve many developmental milestones such as sitting unsupported and speaking. Many affected infants also have difficulty feeding. The seizures in phosphoglycerate dehydrogenase deficiency can vary in type. Recurrent muscle contractions called infantile spasms are typical early in the disorder. Without early treatment, seizures may progress to tonic-clonic seizures, which involve a loss of consciousness, muscle rigidity, and convulsions; myoclonic seizures, which involve rapid, uncontrolled muscle jerks; or drop attacks, which are sudden episodes of weak muscle tone. Individuals with the infantile form of phosphoglycerate dehydrogenase deficiency develop many of the features described above. Individuals with the juvenile form typically have epilepsy as well as mild developmental delay and intellectual disability. Only one case of the adult form has been reported; signs and symptoms began in mid-adulthood and included mild intellectual disability; difficulty coordinating movements (ataxia); and numbness, tingling, and pain in the arms and legs (sensory neuropathy).

MalaCards based summary : Phosphoglycerate Dehydrogenase Deficiency, also known as phgdh deficiency, is related to phosphoserine aminotransferase deficiency and phosphoserine phosphatase deficiency, 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 Carbon metabolism. Affiliated tissues include brain, testes and endothelial, and related phenotypes are hyposerinemia and hypoglycinemia

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 : 56 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)

KEGG : 36 3-Phosphoglycerate dehydrogenase (3-PGDH) deficiency is a rare autosomal recessive disorder caused by a defect in the synthesis of the amino acid L-serine characterized clinically by congenital microcephaly, psychomotor retardation, and infantile onset of intractable seizures. The biochemical abnormalities associated with this disorder are low concentrations of L-serine, D-serine, and glycine in cerebrospinal fluid (CSF) and plasma. Mutations have been identified in PHGDH, the gene encoding 3-PGDH.

UniProtKB/Swiss-Prot : 73 Phosphoglycerate dehydrogenase deficiency: An autosomal recessive inborn error of L-serine biosynthesis, clinically characterized by congenital microcephaly, psychomotor retardation, and seizures.

Wikipedia : 74 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 33)
# Related Disease Score Top Affiliating Genes
1 phosphoserine aminotransferase deficiency 31.9 PSPH PSAT1 PHGDH
2 phosphoserine phosphatase deficiency 30.2 PSPH PHGDH
3 neu-laxova syndrome 1 30.2 PSPH PSAT1 PHGDH
4 serine deficiency 30.1 PSPH PSAT1 PHGDH
5 neu-laxova syndrome due to 3-phosphoglycerate dehydrogenase deficiency 12.6
6 hypertonia 10.3
7 strabismus 10.1
8 west syndrome 10.1
9 hypogonadism 10.1
10 inherited metabolic disorder 10.1
11 mechanical strabismus 10.1
12 aminoacidopathies 10.1
13 neurometabolic disorder due to serine deficiency 10.1
14 autosomal recessive disease 10.1
15 primary microcephaly 10.1
16 epilepsy 10.1
17 alacrima, achalasia, and mental retardation syndrome 10.0
18 microcephaly 10.0
19 visual epilepsy 10.0
20 ichthyosis 10.0
21 seizure disorder 10.0
22 spasticity 10.0
23 ectropion 10.0 PSAT1 PHGDH
24 neuropathy, hereditary sensory and autonomic, type ia 9.9 SPTSSB SPTSSA
25 hereditary sensory and autonomic neuropathy type 1 9.7 SPTSSB SPTSSA
26 microcephaly 16, primary, autosomal recessive 9.6 ZNF335 ANKLE2
27 microcephaly 15, primary, autosomal recessive 9.6 ZNF335 ANKLE2
28 microcephaly 18, primary, autosomal dominant 9.6 ZNF335 ANKLE2
29 microcephaly 10, primary, autosomal recessive 9.5 ZNF335 ANKLE2
30 microcephaly 13, primary, autosomal recessive 9.5 ZNF335 ANKLE2
31 hereditary sensory neuropathy 9.5 SPTSSB SPTSSA
32 microcephaly 17, primary, autosomal recessive 9.5 ZNF335 ANKLE2
33 microcephaly 14, primary, autosomal recessive 9.5 ZNF335 ANKLE2

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



Diseases related to Phosphoglycerate Dehydrogenase Deficiency

Symptoms & Phenotypes for Phosphoglycerate Dehydrogenase Deficiency

Human phenotypes related to Phosphoglycerate Dehydrogenase Deficiency:

58 31 (show top 50) (show all 59)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 hyposerinemia 58 31 hallmark (90%) Very frequent (99-80%) HP:0012279
2 hypoglycinemia 58 31 hallmark (90%) Very frequent (99-80%) HP:0012277
3 short stature 58 31 frequent (33%) Frequent (79-30%) HP:0004322
4 failure to thrive 58 31 frequent (33%) Frequent (79-30%) HP:0001508
5 vomiting 58 31 frequent (33%) Frequent (79-30%) HP:0002013
6 feeding difficulties 58 31 frequent (33%) Frequent (79-30%) HP:0011968
7 developmental stagnation 58 31 frequent (33%) Frequent (79-30%) HP:0007281
8 intrauterine growth retardation 58 31 frequent (33%) Frequent (79-30%) HP:0001511
9 severe global developmental delay 58 31 frequent (33%) Frequent (79-30%) HP:0011344
10 esotropia 58 31 frequent (33%) Frequent (79-30%) HP:0000565
11 cerebral hypomyelination 58 31 frequent (33%) Frequent (79-30%) HP:0006808
12 delayed myelination 58 31 frequent (33%) Frequent (79-30%) HP:0012448
13 cerebral white matter atrophy 58 31 frequent (33%) Frequent (79-30%) HP:0012762
14 congenital microcephaly 58 31 frequent (33%) Frequent (79-30%) HP:0011451
15 epileptic spasm 31 frequent (33%) HP:0011097
16 inguinal hernia 58 31 occasional (7.5%) Occasional (29-5%) HP:0000023
17 umbilical hernia 58 31 occasional (7.5%) Occasional (29-5%) HP:0001537
18 abnormal facial shape 58 31 occasional (7.5%) Occasional (29-5%) HP:0001999
19 gastroesophageal reflux 58 31 occasional (7.5%) Occasional (29-5%) HP:0002020
20 spastic tetraplegia 58 31 occasional (7.5%) Occasional (29-5%) HP:0002510
21 irritability 58 31 occasional (7.5%) Occasional (29-5%) HP:0000737
22 ventriculomegaly 58 31 occasional (7.5%) Occasional (29-5%) HP:0002119
23 adducted thumb 58 31 occasional (7.5%) Occasional (29-5%) HP:0001181
24 moderate global developmental delay 58 31 occasional (7.5%) Occasional (29-5%) HP:0011343
25 hypoplasia of the corpus callosum 58 31 occasional (7.5%) Occasional (29-5%) HP:0002079
26 hypogonadism 58 31 occasional (7.5%) Occasional (29-5%) HP:0000135
27 abnormal cortical gyration 58 31 occasional (7.5%) Occasional (29-5%) HP:0002536
28 athetosis 58 31 occasional (7.5%) Occasional (29-5%) HP:0002305
29 cerebral visual impairment 58 31 occasional (7.5%) Occasional (29-5%) HP:0100704
30 developmental cataract 58 31 occasional (7.5%) Occasional (29-5%) HP:0000519
31 abnormality of hair texture 58 31 occasional (7.5%) Occasional (29-5%) HP:0010719
32 megaloblastic anemia 58 31 occasional (7.5%) Occasional (29-5%) HP:0001889
33 esophagitis 58 31 occasional (7.5%) Occasional (29-5%) HP:0100633
34 atonic seizure 58 31 occasional (7.5%) Occasional (29-5%) HP:0010819
35 inappropriate crying 58 31 occasional (7.5%) Occasional (29-5%) HP:0030215
36 generalized ichthyosis 58 31 occasional (7.5%) Occasional (29-5%) HP:0007503
37 cerebral hypoplasia 31 occasional (7.5%) HP:0006872
38 bilateral tonic-clonic seizure 31 occasional (7.5%) HP:0002069
39 generalized myoclonic seizure 31 occasional (7.5%) HP:0002123
40 generalized non-motor (absence) seizure 31 occasional (7.5%) HP:0002121
41 focal emotional seizure with laughing 31 occasional (7.5%) HP:0010821
42 intellectual disability 31 HP:0001249
43 behavioral abnormality 58 Occasional (29-5%)
44 microcephaly 58 Frequent (79-30%)
45 hypertonia 58 Occasional (29-5%)
46 spasticity 58 Frequent (79-30%)
47 generalized myoclonic seizures 58 Occasional (29-5%)
48 nystagmus 31 HP:0000639
49 growth delay 31 HP:0001510
50 thrombocytopenia 31 HP:0001873

Symptoms via clinical synopsis from OMIM:

56
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

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
2 3-Phosphoglycerate Dehydrogenase Deficiency 29

Anatomical Context for Phosphoglycerate Dehydrogenase Deficiency

MalaCards organs/tissues related to Phosphoglycerate Dehydrogenase Deficiency:

40
Brain, Testes, Endothelial

Publications for Phosphoglycerate Dehydrogenase Deficiency

Articles related to Phosphoglycerate Dehydrogenase Deficiency:

(show all 32)
# Title Authors PMID Year
1
Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency--a neurometabolic disorder associated with reduced L-serine biosynthesis. 56 6 61
11055895 2000
2
Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. 56 6
19235232 2009
3
Infantile Serine Biosynthesis Defect Due to Phosphoglycerate Dehydrogenase Deficiency: Variability in Phenotype and Treatment Response, Novel Mutations, and Diagnostic Challenges. 56 61
28135894 2017
4
Prenatal and early postnatal treatment in 3-phosphoglycerate-dehydrogenase deficiency. 56 61
15610810 2004
5
Congenital microcephaly and seizures due to 3-phosphoglycerate dehydrogenase deficiency: outcome of treatment with amino acids. 61 56
12118526 2002
6
3-phosphoglycerate dehydrogenase deficiency in a patient with West syndrome. 6 61
11034457 2000
7
3-Phosphoglycerate dehydrogenase deficiency: an inborn error of serine biosynthesis. 61 56
8758134 1996
8
Disturbed phospholipid metabolism in serine biosynthesis defects revealed by metabolomic profiling. 56
29269105 2018
9
On the phenotypic spectrum of serine biosynthesis defects. 56
26960553 2016
10
Reduction of stratum corneum ceramides in Neu-Laxova syndrome caused by phosphoglycerate dehydrogenase deficiency. 61
30348640 2018
11
Serine Synthesis via PHGDH Is Essential for Heme Production in Endothelial Cells. 61
30017355 2018
12
Phosphoglycerate dehydrogenase inhibition induces p-mTOR-independent autophagy and promotes multilineage differentiation in embryonal carcinoma stem-like cells. 61
30250195 2018
13
Phosphoglycerate dehydrogenase (PHGDH) deficiency without epilepsy mimicking primary microcephaly. 61
28440900 2017
14
Recurrent and Prolonged Infections in a Child with a Homozygous IFIH1 Nonsense Mutation. 61
29018476 2017
15
Two new cases of serine deficiency disorders treated with l-serine. 61
26610677 2016
16
3-Phosphoglycerate dehydrogenase deficiency: description of two new cases in Tunisia and review of the literature. 61
23564319 2013
17
A serine synthesis defect presenting with a Charcot-Marie-Tooth-like polyneuropathy. 61
22393170 2012
18
Expanding the clinical spectrum of 3-phosphoglycerate dehydrogenase deficiency. 61
21113737 2011
19
3-phosphoglycerate dehydrogenase deficiency: a case report of a treatable cause of seizures. 61
20196394 2009
20
Early onset West syndrome with cerebral hypomyelination and reduced cerebral white matter. 61
18065176 2008
21
D-serine in the developing human central nervous system. 61
17068790 2006
22
Treatment with amino acids in serine deficiency disorders. 61
16763900 2006
23
Reference data for cerebrospinal fluid and the utility of amino acid measurement for the diagnosis of inborn errors of metabolism. 61
16390611 2006
24
Cerebral folate deficiency. 61
15581159 2004
25
Genetic disorders of gamma-aminobutyric acid, glycine, and serine as causes of epilepsy. 61
12597057 2002
26
V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. 61
11751922 2002
27
Phenotypic heterogeneity and adverse effects of serine treatment in 3-phosphoglycerate dehydrogenase deficiency: report on two siblings. 61
11571699 2001
28
Neurotransmitters in 3-phosphoglycerate dehydrogenase deficiency. 61
11131361 2000
29
Hypomyelination and reversible white matter attenuation in 3-phosphoglycerate dehydrogenase deficiency. 61
11508546 2000
30
Continuing education in neurometabolic disorders--serine deficiency disorders. 61
10222452 1999
31
Beneficial effects of L-serine and glycine in the management of seizures in 3-phosphoglycerate dehydrogenase deficiency. 61
9708551 1998
32
3-Phosphoglycerate dehydrogenase deficiency and 3-phosphoserine phosphatase deficiency: inborn errors of serine biosynthesis. 61
8739971 1996

Variations for Phosphoglycerate Dehydrogenase Deficiency

ClinVar genetic disease variations for Phosphoglycerate Dehydrogenase Deficiency:

6 (show top 50) (show all 100) ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 PHGDH NM_006623.4(PHGDH):c.1030C>T (p.Arg344Ter)SNV Pathogenic 522743 rs769256568 1:120283093-120283093 1:119740470-119740470
2 PHGDH NM_006623.4(PHGDH):c.958_968del (p.Ala320fs)deletion Pathogenic 848472 1:120283017-120283027 1:119740394-119740404
3 PHGDH NM_006623.4(PHGDH):c.1286G>T (p.Gly429Val)SNV Pathogenic 916534 1:120285506-120285506 1:119742883-119742883
4 PHGDH NM_006623.4(PHGDH):c.138+2dupduplication Pathogenic 916535 1:120254784-120254785 1:119712161-119712162
5 PHGDH NM_006623.4(PHGDH):c.1468G>A (p.Val490Met)SNV Pathogenic 3867 rs121907987 1:120286529-120286529 1:119743906-119743906
6 PHGDH NM_006623.4(PHGDH):c.1273G>A (p.Val425Met)SNV Pathogenic 3868 rs121907988 1:120285493-120285493 1:119742870-119742870
7 PHGDH NM_006623.4(PHGDH):c.714del (p.Ile239fs)deletion Pathogenic 3869 rs730882181 1:120277986-120277986 1:119735363-119735363
8 PHGDH NM_006623.4(PHGDH):c.1129G>A (p.Gly377Ser)SNV Pathogenic 3871 rs267606948 1:120284440-120284440 1:119741817-119741817
9 PHGDH NM_006623.4(PHGDH):c.781G>A (p.Val261Met)SNV Likely pathogenic 3872 rs267606947 1:120278055-120278055 1:119735432-119735432
10 PHGDH NM_006623.4(PHGDH):c.1078+1G>ASNV Likely pathogenic 836495 1:120283142-120283142 1:119740519-119740519
11 PHGDH NC_000001.11:g.(?_119743876)_(119744050_?)deldeletion Likely pathogenic 830944 1:120286499-120286673
12 PHGDH NM_006623.4(PHGDH):c.797C>T (p.Pro266Leu)SNV Likely pathogenic 522677 rs775936961 1:120279741-120279741 1:119737118-119737118
13 PHGDH NM_006623.4(PHGDH):c.519G>A (p.Gly173=)SNV Conflicting interpretations of pathogenicity 749092 1:120277265-120277265 1:119734642-119734642
14 PHGDH NM_006623.4(PHGDH):c.1559C>A (p.Ala520Glu)SNV Conflicting interpretations of pathogenicity 719978 1:120286620-120286620 1:119743997-119743997
15 PHGDH NM_006623.4(PHGDH):c.403C>T (p.Arg135Trp)SNV Conflicting interpretations of pathogenicity 3870 rs267606949 1:120269520-120269520 1:119726897-119726897
16 PHGDH NM_006623.4(PHGDH):c.834C>A (p.Val278=)SNV Conflicting interpretations of pathogenicity 292315 rs147866831 1:120279778-120279778 1:119737155-119737155
17 PHGDH NM_006623.4(PHGDH):c.372G>A (p.Ala124=)SNV Conflicting interpretations of pathogenicity 292308 rs146740411 1:120269489-120269489 1:119726866-119726866
18 PHGDH NM_006623.4(PHGDH):c.1257G>A (p.Gly419=)SNV Conflicting interpretations of pathogenicity 292319 rs374303746 1:120285477-120285477 1:119742854-119742854
19 PHGDH NM_006623.4(PHGDH):c.*165_*166insGTAGinsertion Uncertain significance 292322 rs140037378 1:120286828-120286829 1:119744205-119744206
20 PHGDH NM_006623.4(PHGDH):c.644-12G>ASNV Uncertain significance 292314 rs370255821 1:120277906-120277906 1:119735283-119735283
21 PHGDH NM_006623.4(PHGDH):c.-79T>CSNV Uncertain significance 292301 rs747803505 1:120254567-120254567 1:119711944-119711944
22 PHGDH NM_006623.3(PHGDH):c.-183G>ASNV Uncertain significance 292298 rs886045202 1:120254463-120254463 1:119711840-119711840
23 PHGDH NM_006623.4(PHGDH):c.381G>A (p.Ser127=)SNV Uncertain significance 292309 rs886045205 1:120269498-120269498 1:119726875-119726875
24 PHGDH NM_006623.4(PHGDH):c.543G>A (p.Glu181=)SNV Uncertain significance 292312 rs886045206 1:120277289-120277289 1:119734666-119734666
25 PHGDH NM_006623.4(PHGDH):c.1158G>A (p.Ala386=)SNV Uncertain significance 292318 rs144484007 1:120284469-120284469 1:119741846-119741846
26 PHGDH NM_006623.4(PHGDH):c.1285G>C (p.Gly429Arg)SNV Uncertain significance 292320 rs145854744 1:120285505-120285505 1:119742882-119742882
27 PHGDH NM_006623.4(PHGDH):c.916A>G (p.Met306Val)SNV Uncertain significance 292316 rs587648058 1:120279860-120279860 1:119737237-119737237
28 PHGDH NM_006623.4(PHGDH):c.390C>T (p.Asp130=)SNV Uncertain significance 292310 rs148078511 1:120269507-120269507 1:119726884-119726884
29 PHGDH NM_006623.3(PHGDH):c.-222G>ASNV Uncertain significance 292296 rs60544490 1:120254424-120254424 1:119711801-119711801
30 PHGDH NM_006623.4(PHGDH):c.-11C>TSNV Uncertain significance 292302 rs886045203 1:120254635-120254635 1:119712012-119712012
31 PHGDH NM_006623.4(PHGDH):c.138G>A (p.Gln46=)SNV Uncertain significance 292303 rs143217390 1:120254783-120254783 1:119712160-119712160
32 PHGDH NM_006623.4(PHGDH):c.1078+10G>TSNV Uncertain significance 292317 rs374994783 1:120283151-120283151 1:119740528-119740528
33 PHGDH NM_006623.4(PHGDH):c.488G>A (p.Arg163Gln)SNV Uncertain significance 139535 rs587777483 1:120269703-120269703 1:119727080-119727080
34 PHGDH NM_006623.3(PHGDH):c.-207G>ASNV Uncertain significance 292297 rs150128831 1:120254439-120254439 1:119711816-119711816
35 PHGDH NM_006623.4(PHGDH):c.694G>A (p.Val232Met)SNV Uncertain significance 859243 1:120277968-120277968 1:119735345-119735345
36 PHGDH NM_006623.4(PHGDH):c.718G>A (p.Val240Met)SNV Uncertain significance 854616 1:120277992-120277992 1:119735369-119735369
37 PHGDH NM_006623.4(PHGDH):c.412-15C>TSNV Uncertain significance 875372 1:120269612-120269612 1:119726989-119726989
38 PHGDH NM_006623.4(PHGDH):c.511-13T>GSNV Uncertain significance 876405 1:120277244-120277244 1:119734621-119734621
39 PHGDH NM_006623.4(PHGDH):c.400G>A (p.Glu134Lys)SNV Uncertain significance 875371 1:120269517-120269517 1:119726894-119726894
40 PHGDH NM_006623.4(PHGDH):c.476A>G (p.Glu159Gly)SNV Uncertain significance 875373 1:120269691-120269691 1:119727068-119727068
41 PHGDH NM_006623.4(PHGDH):c.507G>A (p.Met169Ile)SNV Uncertain significance 875374 1:120269722-120269722 1:119727099-119727099
42 PHGDH NM_006623.4(PHGDH):c.808C>T (p.Arg270Trp)SNV Uncertain significance 874454 1:120279752-120279752 1:119737129-119737129
43 PHGDH NM_006623.4(PHGDH):c.809G>A (p.Arg270Gln)SNV Uncertain significance 874455 1:120279753-120279753 1:119737130-119737130
44 PHGDH NM_006623.4(PHGDH):c.*8G>ASNV Uncertain significance 874503 1:120286671-120286671 1:119744048-119744048
45 PHGDH NM_006623.4(PHGDH):c.*28G>ASNV Uncertain significance 874504 1:120286691-120286691 1:119744068-119744068
46 PHGDH NM_006623.4(PHGDH):c.*58G>CSNV Uncertain significance 875428 1:120286721-120286721 1:119744098-119744098
47 PHGDH NM_006623.4(PHGDH):c.*140A>GSNV Uncertain significance 875429 1:120286803-120286803 1:119744180-119744180
48 PHGDH NM_006623.4(PHGDH):c.1471C>T (p.Arg491Trp)SNV Uncertain significance 496330 rs587731325 1:120286532-120286532 1:119743909-119743909
49 PHGDH NM_006623.4(PHGDH):c.743C>A (p.Ala248Asp)SNV Uncertain significance 536420 rs201782441 1:120278017-120278017 1:119735394-119735394
50 PHGDH NM_006623.4(PHGDH):c.411+5G>TSNV Uncertain significance 565930 rs775568707 1:120269533-120269533 1:119726910-119726910

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

73
# 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 rs201553627
5 PHGDH p.Gly377Ser VAR_059029 rs267606948
6 PHGDH p.Val490Met VAR_059030 rs121907987

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

Cellular components related to Phosphoglycerate Dehydrogenase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 serine C-palmitoyltransferase complex GO:0017059 8.62 SPTSSB SPTSSA

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

# Name GO ID Score Top Affiliating Genes
1 neurogenesis GO:0022008 9.4 PHGDH BHLHE22
2 sphingolipid metabolic process GO:0006665 9.37 SPTSSB SPTSSA
3 sphingolipid biosynthetic process GO:0030148 9.32 SPTSSB SPTSSA
4 ceramide biosynthetic process GO:0046513 9.26 SPTSSB SPTSSA
5 L-serine metabolic process GO:0006563 9.16 PSPH PHGDH
6 cellular amino acid biosynthetic process GO:0008652 9.13 PSPH PSAT1 PHGDH
7 L-serine biosynthetic process GO:0006564 8.8 PSPH PSAT1 PHGDH

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

# Name GO ID Score Top Affiliating Genes
1 serine C-palmitoyltransferase activity GO:0004758 8.62 SPTSSB SPTSSA

Sources for Phosphoglycerate Dehydrogenase Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
53 NINDS
54 Novoseek
56 OMIM
57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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