MCID: PHS023
MIFTS: 30

Phosphoserine Aminotransferase Deficiency

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

Aliases & Classifications for Phosphoserine Aminotransferase Deficiency

MalaCards integrated aliases for Phosphoserine Aminotransferase Deficiency:

Name: Phosphoserine Aminotransferase Deficiency 57 12 53 59 75 29 13 6 73
Psat Deficiency 57 12 53 59 15
Psatd 57 75
Phosphoserine Aminotransferase Deficiency 37
Deficiency, Phosphoserine Aminotransferase 40

Characteristics:

Orphanet epidemiological data:

59
phosphoserine aminotransferase deficiency
Inheritance: Autosomal dominant; Age of onset: Infancy,Neonatal;

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
onset in infancy
treatment with serine and glycine replacement may alleviate features if started at birth
lack of treatment results in early death


HPO:

32
phosphoserine aminotransferase deficiency:
Onset and clinical course infantile onset
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 57 610992
Disease Ontology 12 DOID:0050723
Orphanet 59 ORPHA284417
ICD10 via Orphanet 34 E72.8
UMLS via Orphanet 74 C1970253
MedGen 42 C1970253
KEGG 37 H01082
UMLS 73 C1970253

Summaries for Phosphoserine Aminotransferase Deficiency

NIH Rare Diseases : 53 The following summary is from Orphanet, a European reference portal for information on rare diseases and orphan drugs.Orpha Number: 284417Disease definitionPhosphoserine aminotransferase deficiency is an extremely rare form of serine deficiency syndrome (see this term) characterized clinically in the two reported cases to date by acquired microcephaly, psychomotor retardation, intractable seizures and hypertonia.Visit the Orphanet disease page for more resources.

MalaCards based summary : Phosphoserine Aminotransferase Deficiency, also known as psat deficiency, is related to neu-laxova syndrome 1 and granulomatous amebic encephalitis, and has symptoms including seizures and posturing. An important gene associated with Phosphoserine Aminotransferase Deficiency is PSAT1 (Phosphoserine Aminotransferase 1), and among its related pathways/superpathways are Glycine, serine and threonine metabolism and Vitamin B6 metabolism. Affiliated tissues include brain, and related phenotypes are seizures and global developmental delay

Disease Ontology : 12 A serine deficiency that has material basis in deficiency of phosphoserine aminotransferase and is characterized by low concentartions of serine and flycine in plasma and cerebrospinal fluid.

OMIM : 57 Deficiency of phosphoserine aminotransferase (PSAT) is characterized biochemically by low plasma and cerebrospinal fluid (CSF) concentrations of serine and glycine and clinically by intractable seizures, acquired microcephaly, hypertonia, and psychomotor retardation. Outcome is poor once the individual becomes symptomatic, but treatment with serine and glycine supplementation from birth can lead to a normal outcome (Hart et al., 2007). (610992)

UniProtKB/Swiss-Prot : 75 Phosphoserine aminotransferase deficiency: Characterized biochemically by low plasma and cerebrospinal fluid concentrations of serine and glycine and clinically by intractable seizures, acquired microcephaly, hypertonia, and psychomotor retardation.

Related Diseases for Phosphoserine Aminotransferase Deficiency

Diseases related to Phosphoserine Aminotransferase Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 neu-laxova syndrome 1 9.6 PHGDH PSAT1
2 granulomatous amebic encephalitis 9.5 PHGDH PSAT1
3 phosphoserine phosphatase deficiency 9.0 PHGDH PSPH
4 serine deficiency 8.7 PHGDH PSAT1 PSPH

Symptoms & Phenotypes for Phosphoserine Aminotransferase Deficiency

Symptoms via clinical synopsis from OMIM:

57
Neurologic Central Nervous System:
hypertonia
psychomotor retardation
hypoplastic cerebellar vermis
seizures, intractable
jerking movements
more
Laboratory Abnormalities:
decreased csf serine
decreased csf glycine
decreased plasma serine
decreased plasma glycine

Abdomen Gastrointestinal:
poor feeding

Head And Neck Head:
microcephaly, acquired


Clinical features from OMIM:

610992

Human phenotypes related to Phosphoserine Aminotransferase Deficiency:

32 (show all 8)
# Description HPO Frequency HPO Source Accession
1 seizures 32 HP:0001250
2 global developmental delay 32 HP:0001263
3 hypertonia 32 HP:0001276
4 cerebellar vermis hypoplasia 32 HP:0001320
5 postnatal microcephaly 32 HP:0005484
6 feeding difficulties in infancy 32 HP:0008872
7 hypoglycinemia 32 HP:0012277
8 hyposerinemia 32 HP:0012279

UMLS symptoms related to Phosphoserine Aminotransferase Deficiency:


seizures, posturing

Drugs & Therapeutics for Phosphoserine Aminotransferase Deficiency

Search Clinical Trials , NIH Clinical Center for Phosphoserine Aminotransferase Deficiency

Genetic Tests for Phosphoserine Aminotransferase Deficiency

Genetic tests related to Phosphoserine Aminotransferase Deficiency:

# Genetic test Affiliating Genes
1 Phosphoserine Aminotransferase Deficiency 29 PSAT1

Anatomical Context for Phosphoserine Aminotransferase Deficiency

MalaCards organs/tissues related to Phosphoserine Aminotransferase Deficiency:

41
Brain

Publications for Phosphoserine Aminotransferase Deficiency

Articles related to Phosphoserine Aminotransferase Deficiency:

# Title Authors Year
1
Phosphoserine aminotransferase deficiency: a novel disorder of the serine biosynthesis pathway. ( 17436247 )
2007

Variations for Phosphoserine Aminotransferase Deficiency

UniProtKB/Swiss-Prot genetic disease variations for Phosphoserine Aminotransferase Deficiency:

75
# Symbol AA change Variation ID SNP ID
1 PSAT1 p.Asp100Ala VAR_037252 rs118203967

ClinVar genetic disease variations for Phosphoserine Aminotransferase Deficiency:

6
(show all 46)
# Gene Variation Type Significance SNP ID Assembly Location
1 PSAT1 NM_058179.3(PSAT1): c.107delG (p.Gly36Alafs) deletion Pathogenic rs587777747 GRCh37 Chromosome 9, 80915564: 80915564
2 PSAT1 NM_058179.3(PSAT1): c.107delG (p.Gly36Alafs) deletion Pathogenic rs587777747 GRCh38 Chromosome 9, 78300648: 78300648
3 PSAT1 NM_058179.3(PSAT1): c.299A> C (p.Asp100Ala) single nucleotide variant Pathogenic rs118203967 GRCh37 Chromosome 9, 80919758: 80919758
4 PSAT1 NM_058179.3(PSAT1): c.299A> C (p.Asp100Ala) single nucleotide variant Pathogenic rs118203967 GRCh38 Chromosome 9, 78304842: 78304842
5 PSAT1 NM_058179.3(PSAT1): c.367A> G (p.Ile123Val) single nucleotide variant Conflicting interpretations of pathogenicity rs116577685 GRCh38 Chromosome 9, 78304910: 78304910
6 PSAT1 NM_058179.3(PSAT1): c.367A> G (p.Ile123Val) single nucleotide variant Conflicting interpretations of pathogenicity rs116577685 GRCh37 Chromosome 9, 80919826: 80919826
7 PSAT1 NM_058179.3(PSAT1): c.*252G> C single nucleotide variant Likely benign rs17064358 GRCh37 Chromosome 9, 80944254: 80944254
8 PSAT1 NM_058179.3(PSAT1): c.*252G> C single nucleotide variant Likely benign rs17064358 GRCh38 Chromosome 9, 78329338: 78329338
9 PSAT1 NM_058179.3(PSAT1): c.*592A> C single nucleotide variant Likely benign rs115361057 GRCh37 Chromosome 9, 80944594: 80944594
10 PSAT1 NM_058179.3(PSAT1): c.*592A> C single nucleotide variant Likely benign rs115361057 GRCh38 Chromosome 9, 78329678: 78329678
11 PSAT1 NM_058179.3(PSAT1): c.*670T> G single nucleotide variant Uncertain significance rs143748888 GRCh38 Chromosome 9, 78329756: 78329756
12 PSAT1 NM_058179.3(PSAT1): c.*670T> G single nucleotide variant Uncertain significance rs143748888 GRCh37 Chromosome 9, 80944672: 80944672
13 PSAT1 NM_058179.3(PSAT1): c.54G> A (p.Pro18=) single nucleotide variant Uncertain significance rs763694865 GRCh37 Chromosome 9, 80912180: 80912180
14 PSAT1 NM_058179.3(PSAT1): c.54G> A (p.Pro18=) single nucleotide variant Uncertain significance rs763694865 GRCh38 Chromosome 9, 78297264: 78297264
15 PSAT1 NM_058179.3(PSAT1): c.55C> G (p.His19Asp) single nucleotide variant Uncertain significance rs1057515669 GRCh37 Chromosome 9, 80912181: 80912181
16 PSAT1 NM_058179.3(PSAT1): c.55C> G (p.His19Asp) single nucleotide variant Uncertain significance rs1057515669 GRCh38 Chromosome 9, 78297265: 78297265
17 PSAT1 NM_058179.3(PSAT1): c.297T> G (p.Ala99=) single nucleotide variant Benign rs3739474 GRCh37 Chromosome 9, 80919756: 80919756
18 PSAT1 NM_058179.3(PSAT1): c.297T> G (p.Ala99=) single nucleotide variant Benign rs3739474 GRCh38 Chromosome 9, 78304840: 78304840
19 PSAT1 NM_058179.3(PSAT1): c.1007+13G> A single nucleotide variant Uncertain significance rs1057515672 GRCh37 Chromosome 9, 80943117: 80943117
20 PSAT1 NM_058179.3(PSAT1): c.1007+13G> A single nucleotide variant Uncertain significance rs1057515672 GRCh38 Chromosome 9, 78328201: 78328201
21 PSAT1 NM_058179.3(PSAT1): c.1008-11G> T single nucleotide variant Uncertain significance rs200199574 GRCh37 Chromosome 9, 80943886: 80943886
22 PSAT1 NM_058179.3(PSAT1): c.1008-11G> T single nucleotide variant Uncertain significance rs200199574 GRCh38 Chromosome 9, 78328970: 78328970
23 PSAT1 NM_058179.3(PSAT1): c.*664A> G single nucleotide variant Uncertain significance rs41277903 GRCh38 Chromosome 9, 78329750: 78329750
24 PSAT1 NM_058179.3(PSAT1): c.*664A> G single nucleotide variant Uncertain significance rs41277903 GRCh37 Chromosome 9, 80944666: 80944666
25 PSAT1 NM_058179.3(PSAT1): c.398-14G> A single nucleotide variant Uncertain significance rs202026355 GRCh37 Chromosome 9, 80921216: 80921216
26 PSAT1 NM_058179.3(PSAT1): c.398-14G> A single nucleotide variant Uncertain significance rs202026355 GRCh38 Chromosome 9, 78306300: 78306300
27 PSAT1 NM_058179.3(PSAT1): c.1059C> T (p.Asp353=) single nucleotide variant Uncertain significance rs115639310 GRCh37 Chromosome 9, 80943948: 80943948
28 PSAT1 NM_058179.3(PSAT1): c.1059C> T (p.Asp353=) single nucleotide variant Uncertain significance rs115639310 GRCh38 Chromosome 9, 78329032: 78329032
29 PSAT1 NM_058179.3(PSAT1): c.*836A> G single nucleotide variant Uncertain significance rs41277905 GRCh38 Chromosome 9, 78329922: 78329922
30 PSAT1 NM_058179.3(PSAT1): c.*836A> G single nucleotide variant Uncertain significance rs41277905 GRCh37 Chromosome 9, 80944838: 80944838
31 PSAT1 NM_058179.3(PSAT1): c.-12G> C single nucleotide variant Benign rs2277148 GRCh37 Chromosome 9, 80912115: 80912115
32 PSAT1 NM_058179.3(PSAT1): c.-12G> C single nucleotide variant Benign rs2277148 GRCh38 Chromosome 9, 78297199: 78297199
33 PSAT1 NM_058179.3(PSAT1): c.43G> C (p.Ala15Pro) single nucleotide variant Uncertain significance rs774962204 GRCh37 Chromosome 9, 80912169: 80912169
34 PSAT1 NM_058179.3(PSAT1): c.43G> C (p.Ala15Pro) single nucleotide variant Uncertain significance rs774962204 GRCh38 Chromosome 9, 78297253: 78297253
35 PSAT1 NM_058179.3(PSAT1): c.571-4dupT duplication Uncertain significance rs1057515670 GRCh37 Chromosome 9, 80923326: 80923326
36 PSAT1 NM_058179.3(PSAT1): c.571-4dupT duplication Uncertain significance rs1057515670 GRCh38 Chromosome 9, 78308410: 78308410
37 PSAT1 NM_058179.3(PSAT1): c.821A> C (p.Lys274Thr) single nucleotide variant Uncertain significance rs1057515671 GRCh37 Chromosome 9, 80932672: 80932672
38 PSAT1 NM_058179.3(PSAT1): c.821A> C (p.Lys274Thr) single nucleotide variant Uncertain significance rs1057515671 GRCh38 Chromosome 9, 78317756: 78317756
39 PSAT1 NM_058179.3(PSAT1): c.*241C> A single nucleotide variant Uncertain significance rs1057515673 GRCh37 Chromosome 9, 80944243: 80944243
40 PSAT1 NM_058179.3(PSAT1): c.*241C> A single nucleotide variant Uncertain significance rs1057515673 GRCh38 Chromosome 9, 78329327: 78329327
41 PSAT1 NM_058179.3(PSAT1): c.*422C> T single nucleotide variant Benign rs10867185 GRCh37 Chromosome 9, 80944424: 80944424
42 PSAT1 NM_058179.3(PSAT1): c.*422C> T single nucleotide variant Benign rs10867185 GRCh38 Chromosome 9, 78329508: 78329508
43 PSAT1 NM_058179.3(PSAT1): c.*789A> G single nucleotide variant Uncertain significance rs1057515674 GRCh38 Chromosome 9, 78329875: 78329875
44 PSAT1 NM_058179.3(PSAT1): c.*789A> G single nucleotide variant Uncertain significance rs1057515674 GRCh37 Chromosome 9, 80944791: 80944791
45 PSAT1 NM_058179.3(PSAT1): c.*865C> G single nucleotide variant Uncertain significance rs529821810 GRCh38 Chromosome 9, 78329951: 78329951
46 PSAT1 NM_058179.3(PSAT1): c.*865C> G single nucleotide variant Uncertain significance rs529821810 GRCh37 Chromosome 9, 80944867: 80944867

Expression for Phosphoserine Aminotransferase Deficiency

Search GEO for disease gene expression data for Phosphoserine Aminotransferase Deficiency.

Pathways for Phosphoserine Aminotransferase Deficiency

Pathways related to Phosphoserine Aminotransferase Deficiency according to KEGG:

37
# Name Kegg Source Accession
1 Glycine, serine and threonine metabolism hsa00260
2 Vitamin B6 metabolism hsa00750

Pathways related to Phosphoserine Aminotransferase Deficiency according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.9 PHGDH PSAT1 PSPH
2
Show member pathways
11.76 PHGDH PSAT1 PSPH
3
Show member pathways
11.48 PHGDH PSAT1 PSPH
4
Show member pathways
10.85 PHGDH PSAT1 PSPH
5
Show member pathways
10.41 PHGDH PSAT1 PSPH

GO Terms for Phosphoserine Aminotransferase Deficiency

Biological processes related to Phosphoserine Aminotransferase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 L-serine metabolic process GO:0006563 9.16 PHGDH PSPH
2 cellular amino acid biosynthetic process GO:0008652 9.13 PHGDH PSAT1 PSPH
3 L-serine biosynthetic process GO:0006564 8.8 PHGDH PSAT1 PSPH

Sources for Phosphoserine Aminotransferase 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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