PSATD
MCID: PHS023
MIFTS: 41

Phosphoserine Aminotransferase Deficiency (PSATD)

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

Aliases & Classifications for Phosphoserine Aminotransferase Deficiency

MalaCards integrated aliases for Phosphoserine Aminotransferase Deficiency:

Name: Phosphoserine Aminotransferase Deficiency 57 12 20 72 36 29 13 6 70
Psat Deficiency 57 12 20 15
Psatd 57 72
Phosphoserine Aminotransferase Deficiency, Infantile/juvenile Form 58
Deficiency, Phosphoserine Aminotransferase 39
Psat Deficiency, Infantile/juvenile Form 58

Characteristics:

Orphanet epidemiological data:

58
phosphoserine aminotransferase deficiency, infantile/juvenile form
Inheritance: Autosomal dominant; Age of onset: Infancy,Neonatal;

OMIM®:

57 (Updated 05-Apr-2021)
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:

31
phosphoserine aminotransferase deficiency:
Inheritance autosomal recessive inheritance
Onset and clinical course infantile onset


Classifications:

Orphanet: 58  
Rare neurological diseases
Inborn errors of metabolism


Summaries for Phosphoserine Aminotransferase Deficiency

KEGG : 36 Phosphoserine aminotransferase (PSAT) deficiency is a disorder of serine biosynthesis characterized biochemically by low plasma and CSF concentrations of serine and glycine and clinically by intractable seizures, acquired microcephaly, hypertonia, and psychomotor retardation. The biochemical and clinical features of PSAT deficiency shared some of the features of 3-PGDH deficiency [DS:H01079]. Mutations in the PSAT1 gene have been identified.

MalaCards based summary : Phosphoserine Aminotransferase Deficiency, also known as psat deficiency, is related to serine deficiency and microcephaly, 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 eye and brain, and related phenotypes are failure to thrive in infancy and profound 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.

GARD : 20 The following summary is from Orphanet, a European reference portal for information on rare diseases and orphan drugs. Orpha Number: 284417 Definition Phosphoserine 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.

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) (Updated 05-Apr-2021)

UniProtKB/Swiss-Prot : 72 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

Graphical network of the top 20 diseases related to Phosphoserine Aminotransferase Deficiency:



Diseases related to Phosphoserine Aminotransferase Deficiency

Symptoms & Phenotypes for Phosphoserine Aminotransferase Deficiency

Human phenotypes related to Phosphoserine Aminotransferase Deficiency:

58 31 (show all 46)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 failure to thrive in infancy 58 31 hallmark (90%) Very frequent (99-80%) HP:0001531
2 profound global developmental delay 58 31 hallmark (90%) Very frequent (99-80%) HP:0012736
3 inappropriate crying 58 31 hallmark (90%) Very frequent (99-80%) HP:0030215
4 hyperglycinemia 58 31 hallmark (90%) Very frequent (99-80%) HP:0002154
5 congenital microcephaly 58 31 hallmark (90%) Very frequent (99-80%) HP:0011451
6 hyposerinemia 58 31 hallmark (90%) Very frequent (99-80%) HP:0012279
7 hyperreflexia 58 31 frequent (33%) Frequent (79-30%) HP:0001347
8 intrauterine growth retardation 58 31 frequent (33%) Frequent (79-30%) HP:0001511
9 thickened nuchal skin fold 58 31 frequent (33%) Frequent (79-30%) HP:0000474
10 hypoplasia of the corpus callosum 58 31 frequent (33%) Frequent (79-30%) HP:0002079
11 cerebral white matter hypoplasia 58 31 frequent (33%) Frequent (79-30%) HP:0012430
12 infantile axial hypotonia 58 31 frequent (33%) Frequent (79-30%) HP:0009062
13 short neck 58 31 occasional (7.5%) Occasional (29-5%) HP:0000470
14 depressed nasal bridge 58 31 occasional (7.5%) Occasional (29-5%) HP:0005280
15 hypertelorism 58 31 occasional (7.5%) Occasional (29-5%) HP:0000316
16 ichthyosis 58 31 occasional (7.5%) Occasional (29-5%) HP:0008064
17 myoclonus 58 31 occasional (7.5%) Occasional (29-5%) HP:0001336
18 micrognathia 58 31 occasional (7.5%) Occasional (29-5%) HP:0000347
19 craniosynostosis 58 31 occasional (7.5%) Occasional (29-5%) HP:0001363
20 sloping forehead 58 31 occasional (7.5%) Occasional (29-5%) HP:0000340
21 paroxysmal involuntary eye movements 58 31 occasional (7.5%) Occasional (29-5%) HP:0007704
22 ankle flexion contracture 58 31 occasional (7.5%) Occasional (29-5%) HP:0006466
23 bilateral talipes equinovarus 58 31 occasional (7.5%) Occasional (29-5%) HP:0001776
24 spastic tetraparesis 58 31 occasional (7.5%) Occasional (29-5%) HP:0001285
25 lissencephaly 58 31 occasional (7.5%) Occasional (29-5%) HP:0001339
26 knee flexion contracture 58 31 occasional (7.5%) Occasional (29-5%) HP:0006380
27 cerebellar vermis hypoplasia 58 31 occasional (7.5%) Occasional (29-5%) HP:0001320
28 gastrostomy tube feeding in infancy 58 31 occasional (7.5%) Occasional (29-5%) HP:0011471
29 delayed myelination 58 31 occasional (7.5%) Occasional (29-5%) HP:0012448
30 simplified gyral pattern 58 31 occasional (7.5%) Occasional (29-5%) HP:0009879
31 eeg with polyspike wave complexes 58 31 occasional (7.5%) Occasional (29-5%) HP:0002392
32 dilation of lateral ventricles 58 31 occasional (7.5%) Occasional (29-5%) HP:0006956
33 nasogastric tube feeding 58 31 occasional (7.5%) Occasional (29-5%) HP:0040288
34 eeg with focal sharp waves 58 31 occasional (7.5%) Occasional (29-5%) HP:0011196
35 cyanotic episode 58 31 occasional (7.5%) Occasional (29-5%) HP:0200048
36 epileptic spasm 31 occasional (7.5%) HP:0011097
37 hypertonia 58 31 Frequent (79-30%) HP:0001276
38 feeding difficulties in infancy 58 31 Very frequent (99-80%) HP:0008872
39 seizures 58 Frequent (79-30%)
40 global developmental delay 31 HP:0001263
41 psychomotor retardation 31 HP:0025356
42 postnatal microcephaly 31 HP:0005484
43 epileptic spasms 58 Occasional (29-5%)
44 hypoglycinemia 31 HP:0012277
45 limb joint contracture 58 Occasional (29-5%)
46 seizure 31 HP:0001250

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Neurologic Central Nervous System:
hypertonia
psychomotor retardation
posturing
seizures, intractable
hypoplastic cerebellar vermis
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 (Updated 05-Apr-2021)

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:

40
Eye, Brain

Publications for Phosphoserine Aminotransferase Deficiency

Articles related to Phosphoserine Aminotransferase Deficiency:

# Title Authors PMID Year
1
Phosphoserine aminotransferase deficiency: a novel disorder of the serine biosynthesis pathway. 57 6 61
17436247 2007
2
Disturbed phospholipid metabolism in serine biosynthesis defects revealed by metabolomic profiling. 57 61
29269105 2018
3
Phosphoserine aminotransferase deficiency: imaging findings in a child with congenital microcephaly. 61
30122079 2020
4
An update on serine deficiency disorders. 61
23463425 2013

Variations for Phosphoserine Aminotransferase Deficiency

ClinVar genetic disease variations for Phosphoserine Aminotransferase Deficiency:

6 (show top 50) (show all 57)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 PSAT1 NM_058179.4(PSAT1):c.107del (p.Gly36fs) Deletion Pathogenic 1081 rs587777747 GRCh37: 9:80915563-80915563
GRCh38: 9:78300647-78300647
2 PSAT1 NM_058179.4(PSAT1):c.299A>C (p.Asp100Ala) SNV Pathogenic 1082 rs118203967 GRCh37: 9:80919758-80919758
GRCh38: 9:78304842-78304842
3 PSAT1 NM_058179.4(PSAT1):c.121+5G>A SNV Likely pathogenic 802488 rs372232840 GRCh37: 9:80915583-80915583
GRCh38: 9:78300667-78300667
4 PSAT1 NM_058179.4(PSAT1):c.1111T>C (p.Ter371Arg) SNV Uncertain significance 632050 rs756701004 GRCh37: 9:80944000-80944000
GRCh38: 9:78329084-78329084
5 PSAT1 NM_058179.4(PSAT1):c.571-4dup Duplication Uncertain significance 367457 rs536197677 GRCh37: 9:80923321-80923322
GRCh38: 9:78308405-78308406
6 PSAT1 NM_058179.4(PSAT1):c.*241C>A SNV Uncertain significance 367462 rs1057515673 GRCh37: 9:80944243-80944243
GRCh38: 9:78329327-78329327
7 PSAT1 NM_058179.4(PSAT1):c.420G>T (p.Trp140Cys) SNV Uncertain significance 976478 GRCh37: 9:80921252-80921252
GRCh38: 9:78306336-78306336
8 PSAT1 NM_058179.4(PSAT1):c.955dup (p.Arg319fs) Duplication Uncertain significance 976479 GRCh37: 9:80943046-80943047
GRCh38: 9:78328130-78328131
9 PSAT1 NM_058179.4(PSAT1):c.*252G>A SNV Uncertain significance 912652 GRCh37: 9:80944254-80944254
GRCh38: 9:78329338-78329338
10 PSAT1 NM_058179.4(PSAT1):c.*293A>G SNV Uncertain significance 912653 GRCh37: 9:80944295-80944295
GRCh38: 9:78329379-78329379
11 PSAT1 NM_058179.4(PSAT1):c.*378T>C SNV Uncertain significance 912654 GRCh37: 9:80944380-80944380
GRCh38: 9:78329464-78329464
12 PSAT1 NM_058179.4(PSAT1):c.107G>A (p.Gly36Asp) SNV Uncertain significance 913714 GRCh37: 9:80915564-80915564
GRCh38: 9:78300648-78300648
13 PSAT1 NM_058179.4(PSAT1):c.231A>T (p.Gly77=) SNV Uncertain significance 913715 GRCh37: 9:80919690-80919690
GRCh38: 9:78304774-78304774
14 PSAT1 NM_058179.4(PSAT1):c.270C>T (p.Leu90=) SNV Uncertain significance 913716 GRCh37: 9:80919729-80919729
GRCh38: 9:78304813-78304813
15 PSAT1 NM_058179.4(PSAT1):c.*496A>G SNV Uncertain significance 913754 GRCh37: 9:80944498-80944498
GRCh38: 9:78329582-78329582
16 PSAT1 NM_058179.4(PSAT1):c.*498C>T SNV Uncertain significance 913755 GRCh37: 9:80944500-80944500
GRCh38: 9:78329584-78329584
17 PSAT1 NM_058179.4(PSAT1):c.*554G>A SNV Uncertain significance 913756 GRCh37: 9:80944556-80944556
GRCh38: 9:78329640-78329640
18 PSAT1 NM_058179.4(PSAT1):c.398-7G>A SNV Uncertain significance 914105 GRCh37: 9:80921223-80921223
GRCh38: 9:78306307-78306307
19 PSAT1 NM_058179.4(PSAT1):c.*719G>A SNV Uncertain significance 914154 GRCh37: 9:80944721-80944721
GRCh38: 9:78329805-78329805
20 PSAT1 NM_058179.4(PSAT1):c.*939C>T SNV Uncertain significance 914155 GRCh37: 9:80944941-80944941
GRCh38: 9:78330025-78330025
21 PSAT1 NM_058179.4(PSAT1):c.-26T>G SNV Uncertain significance 914574 GRCh37: 9:80912101-80912101
GRCh38: 9:78297185-78297185
22 PSAT1 NM_058179.4(PSAT1):c.*836A>G SNV Uncertain significance 367469 rs41277905 GRCh37: 9:80944838-80944838
GRCh38: 9:78329922-78329922
23 PSAT1 NM_058179.4(PSAT1):c.*664A>G SNV Uncertain significance 367466 rs41277903 GRCh37: 9:80944666-80944666
GRCh38: 9:78329750-78329750
24 PSAT1 NM_058179.4(PSAT1):c.54G>A (p.Pro18=) SNV Uncertain significance 367452 rs763694865 GRCh37: 9:80912180-80912180
GRCh38: 9:78297264-78297264
25 PSAT1 NM_058179.4(PSAT1):c.*670T>G SNV Uncertain significance 367467 rs143748888 GRCh37: 9:80944672-80944672
GRCh38: 9:78329756-78329756
26 PSAT1 NM_058179.4(PSAT1):c.1007+13G>A SNV Uncertain significance 367459 rs1057515672 GRCh37: 9:80943117-80943117
GRCh38: 9:78328201-78328201
27 PSAT1 NM_058179.4(PSAT1):c.398-14G>A SNV Uncertain significance 367456 rs202026355 GRCh37: 9:80921216-80921216
GRCh38: 9:78306300-78306300
28 PSAT1 NM_058179.4(PSAT1):c.*789A>G SNV Uncertain significance 367468 rs1057515674 GRCh37: 9:80944791-80944791
GRCh38: 9:78329875-78329875
29 PSAT1 NM_058179.4(PSAT1):c.61-2A>G SNV Uncertain significance 632049 rs1564012047 GRCh37: 9:80915516-80915516
GRCh38: 9:78300600-78300600
30 PSAT1 NM_058179.4(PSAT1):c.10C>G (p.Pro4Ala) SNV Uncertain significance 912615 GRCh37: 9:80912136-80912136
GRCh38: 9:78297220-78297220
31 PSAT1 NM_058179.4(PSAT1):c.1074C>T (p.Ala358=) SNV Uncertain significance 912649 GRCh37: 9:80943963-80943963
GRCh38: 9:78329047-78329047
32 PSAT1 NM_058179.4(PSAT1):c.*219A>G SNV Uncertain significance 912650 GRCh37: 9:80944221-80944221
GRCh38: 9:78329305-78329305
33 PSAT1 NM_058179.4(PSAT1):c.821A>C (p.Lys274Thr) SNV Uncertain significance 367458 rs1057515671 GRCh37: 9:80932672-80932672
GRCh38: 9:78317756-78317756
34 PSAT1 NM_058179.4(PSAT1):c.55C>G (p.His19Asp) SNV Uncertain significance 367453 rs1057515669 GRCh37: 9:80912181-80912181
GRCh38: 9:78297265-78297265
35 PSAT1 NM_058179.4(PSAT1):c.43G>C (p.Ala15Pro) SNV Uncertain significance 367451 rs774962204 GRCh37: 9:80912169-80912169
GRCh38: 9:78297253-78297253
36 PSAT1 NM_058179.4(PSAT1):c.4G>T (p.Asp2Tyr) SNV Uncertain significance 912614 GRCh37: 9:80912130-80912130
GRCh38: 9:78297214-78297214
37 PSAT1 NM_058179.4(PSAT1):c.104T>A (p.Val35Asp) SNV Uncertain significance 912616 GRCh37: 9:80915561-80915561
GRCh38: 9:78300645-78300645
38 PSAT1 NM_058179.4(PSAT1):c.335C>T (p.Ala112Val) SNV Uncertain significance 913717 GRCh37: 9:80919794-80919794
GRCh38: 9:78304878-78304878
39 PSAT1 NM_058179.4(PSAT1):c.370G>A (p.Val124Ile) SNV Uncertain significance 914104 GRCh37: 9:80919829-80919829
GRCh38: 9:78304913-78304913
40 PSAT1 NM_058179.4(PSAT1):c.445G>A (p.Val149Met) SNV Uncertain significance 914106 GRCh37: 9:80921277-80921277
GRCh38: 9:78306361-78306361
41 PSAT1 NM_058179.4(PSAT1):c.499G>A (p.Asp167Asn) SNV Uncertain significance 914107 GRCh37: 9:80921331-80921331
GRCh38: 9:78306415-78306415
42 PSAT1 NM_058179.4(PSAT1):c.665G>A (p.Arg222Gln) SNV Uncertain significance 914108 GRCh37: 9:80923424-80923424
GRCh38: 9:78308508-78308508
43 PSAT1 NM_058179.4(PSAT1):c.700G>T (p.Ala234Ser) SNV Uncertain significance 914109 GRCh37: 9:80923459-80923459
GRCh38: 9:78308543-78308543
44 PSAT1 NM_058179.4(PSAT1):c.706A>C (p.Asn236His) SNV Uncertain significance 914615 GRCh37: 9:80923465-80923465
GRCh38: 9:78308549-78308549
45 PSAT1 NM_058179.4(PSAT1):c.916C>T (p.Arg306Cys) SNV Uncertain significance 542039 rs113824905 GRCh37: 9:80943013-80943013
GRCh38: 9:78328097-78328097
46 PSAT1 NM_058179.4(PSAT1):c.677C>T (p.Ser226Leu) SNV Uncertain significance 976999 GRCh37: 9:80923436-80923436
GRCh38: 9:78308520-78308520
47 PSAT1 NM_058179.4(PSAT1):c.793G>A (p.Ala265Thr) SNV Uncertain significance 976898 GRCh37: 9:80932644-80932644
GRCh38: 9:78317728-78317728
48 PSAT1 NM_058179.4(PSAT1):c.367A>G (p.Ile123Val) SNV Likely benign 367455 rs116577685 GRCh37: 9:80919826-80919826
GRCh38: 9:78304910-78304910
49 PSAT1 NM_058179.4(PSAT1):c.*865C>G SNV Likely benign 367470 rs529821810 GRCh37: 9:80944867-80944867
GRCh38: 9:78329951-78329951
50 PSAT1 NM_058179.4(PSAT1):c.*592A>C SNV Likely benign 367465 rs115361057 GRCh37: 9:80944594-80944594
GRCh38: 9:78329678-78329678

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

72
# Symbol AA change Variation ID SNP ID
1 PSAT1 p.Asp100Ala VAR_037252 rs118203967

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:

36
# 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
13.6 SUOX PSPH PSAT1 PHGDH GCAT BTD
2
Show member pathways
13.28 SUOX PSPH PSAT1 PHGDH GCAT AMT
3
Show member pathways
11.88 PSPH PSAT1 PHGDH AMT
4
Show member pathways
11.6 SUOX PSAT1 PHGDH
5
Show member pathways
11.41 PSPH PSAT1 PHGDH AMT
6
Show member pathways
10.94 PSPH PSAT1 PHGDH
7
Show member pathways
10.74 PSPH PSAT1 PHGDH GCAT AMT

GO Terms for Phosphoserine Aminotransferase Deficiency

Cellular components related to Phosphoserine Aminotransferase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 mitochondrial matrix GO:0005759 8.8 SUOX BTD AMT

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

# Name GO ID Score Top Affiliating Genes
1 cellular amino acid metabolic process GO:0006520 9.32 PHGDH GCAT
2 tRNA splicing, via endonucleolytic cleavage and ligation GO:0006388 9.26 TSEN54 TSEN15
3 L-serine metabolic process GO:0006563 9.16 PSPH PHGDH
4 cellular amino acid biosynthetic process GO:0008652 9.13 PSPH PSAT1 PHGDH
5 L-serine biosynthetic process GO:0006564 8.8 PSPH PSAT1 PHGDH

Molecular functions related to Phosphoserine Aminotransferase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 pyridoxal phosphate binding GO:0030170 8.96 PSAT1 GCAT
2 transaminase activity GO:0008483 8.62 PSAT1 AMT

Sources for Phosphoserine Aminotransferase Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
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
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Apr-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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