PSPHD
MCID: PHS022
MIFTS: 37

Phosphoserine Phosphatase Deficiency (PSPHD)

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

Aliases & Classifications for Phosphoserine Phosphatase Deficiency

MalaCards integrated aliases for Phosphoserine Phosphatase Deficiency:

Name: Phosphoserine Phosphatase Deficiency 57 12 72 36 13
Deficiency of Phosphoserine Phosphatase 29 6 70
Psphd 57 12 72
Psph Deficiency 12 15
3-Phosphoserine Phosphatase Deficiency, Infantile/juvenile Form 58
Psph Deficiency, Infantile/juvenile Form 58
Deficiency, Phosphoserine Phosphatase 39

Characteristics:

Orphanet epidemiological data:

58

OMIM®:

57 (Updated 05-Apr-2021)
Inheritance:
autosomal recessive

Miscellaneous:
onset in infancy
two unrelated families have been reported (last curated march 2015)


HPO:

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


Classifications:

Orphanet: 58  
Rare neurological diseases
Inborn errors of metabolism


Summaries for Phosphoserine Phosphatase Deficiency

KEGG : 36 Phosphoserine phosphatase deficiency (PSPHD) has been reported in a boy with pre- and postnatal growth retardation, moderate psychomotor retardation, and facial dysmorphism suggestive of Williams syndrome, and in whom compound heterozygous mutation was later identified in PSPH gene. PSPH is the enzyme catalyzing the final and irreversible step of L-serine synthesis from the glycolytic intermediate, 3-phosphoglycerate.

MalaCards based summary : Phosphoserine Phosphatase Deficiency, also known as deficiency of phosphoserine phosphatase, is related to phosphoglycerate dehydrogenase deficiency and serine deficiency, and has symptoms including seizures An important gene associated with Phosphoserine Phosphatase Deficiency is PSPH (Phosphoserine Phosphatase), and among its related pathways/superpathways are Glycine, serine and threonine metabolism and One carbon pool by folate. Related phenotypes are global developmental delay and postnatal growth retardation

Disease Ontology : 12 A serine deficiency that has material basis in deficiency of phosphoserine phosphatase impeding the synthesis of L-serine.

UniProtKB/Swiss-Prot : 72 Phosphoserine phosphatase deficiency: An autosomal recessive disorder that results in pre- and postnatal growth retardation, moderate psychomotor retardation and facial features suggestive of Williams syndrome.

More information from OMIM: 614023

Related Diseases for Phosphoserine Phosphatase Deficiency

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



Diseases related to Phosphoserine Phosphatase Deficiency

Symptoms & Phenotypes for Phosphoserine Phosphatase Deficiency

Human phenotypes related to Phosphoserine Phosphatase Deficiency:

58 31 (show all 23)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 global developmental delay 58 31 frequent (33%) Frequent (79-30%) HP:0001263
2 postnatal growth retardation 58 31 frequent (33%) Frequent (79-30%) HP:0008897
3 intellectual disability, moderate 58 31 frequent (33%) Frequent (79-30%) HP:0002342
4 feeding difficulties 58 31 frequent (33%) Frequent (79-30%) HP:0011968
5 hyposerinemia 58 31 frequent (33%) Frequent (79-30%) HP:0012279
6 abnormal facial shape 58 31 occasional (7.5%) Occasional (29-5%) HP:0001999
7 microcephaly 58 31 occasional (7.5%) Occasional (29-5%) HP:0000252
8 hypertonia 58 31 occasional (7.5%) Occasional (29-5%) HP:0001276
9 gastroesophageal reflux 58 31 occasional (7.5%) Occasional (29-5%) HP:0002020
10 full cheeks 58 31 occasional (7.5%) Occasional (29-5%) HP:0000293
11 micrognathia 58 31 occasional (7.5%) Occasional (29-5%) HP:0000347
12 palpebral edema 58 31 occasional (7.5%) Occasional (29-5%) HP:0100540
13 wide mouth 58 31 occasional (7.5%) Occasional (29-5%) HP:0000154
14 hypospadias 58 31 occasional (7.5%) Occasional (29-5%) HP:0000047
15 broad forehead 58 31 occasional (7.5%) Occasional (29-5%) HP:0000337
16 esophagitis 58 31 occasional (7.5%) Occasional (29-5%) HP:0100633
17 narrow forehead 58 31 occasional (7.5%) Occasional (29-5%) HP:0000341
18 cerebral atrophy 31 occasional (7.5%) HP:0002059
19 bilateral tonic-clonic seizure 31 occasional (7.5%) HP:0002069
20 intellectual disability 31 HP:0001249
21 intrauterine growth retardation 31 HP:0001511
22 generalized tonic-clonic seizures 58 Occasional (29-5%)
23 seizure 31 HP:0001250

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Neurologic Central Nervous System:
seizures
hypertonia
mental retardation
delayed development
cerebral atrophy (rare)

Laboratory Abnormalities:
decreased plasma serine
decreased plasma glycine

Head And Neck Head:
microcephaly (rare)

Growth Other:
poor growth (1 patient)

Clinical features from OMIM®:

614023 (Updated 05-Apr-2021)

UMLS symptoms related to Phosphoserine Phosphatase Deficiency:


seizures

Drugs & Therapeutics for Phosphoserine Phosphatase Deficiency

Search Clinical Trials , NIH Clinical Center for Phosphoserine Phosphatase Deficiency

Genetic Tests for Phosphoserine Phosphatase Deficiency

Genetic tests related to Phosphoserine Phosphatase Deficiency:

# Genetic test Affiliating Genes
1 Deficiency of Phosphoserine Phosphatase 29 PSPH

Anatomical Context for Phosphoserine Phosphatase Deficiency

Publications for Phosphoserine Phosphatase Deficiency

Articles related to Phosphoserine Phosphatase Deficiency:

# Title Authors PMID Year
1
Mutations responsible for 3-phosphoserine phosphatase deficiency. 61 57 6
14673469 2004
2
Phosphoserine phosphatase deficiency in a patient with Williams syndrome. 6 57 61
9222972 1997
3
Phosphoserine phosphatase (PSPH) gene mutation in an intellectual disability family from Pakistan. 6 57
25080166 2015
4
Novel Report of Phosphoserine Phosphatase Deficiency in an Adult with Myeloneuropathy and Limb Contractures. 61
26589312 2016
5
Erratum to: Novel Report of Phosphoserine Phosphatase Deficiency in an Adult with Myeloneuropathy and Limb Contractures. 61
26888760 2016
6
Treatment with amino acids in serine deficiency disorders. 61
16763900 2006
7
Continuing education in neurometabolic disorders--serine deficiency disorders. 61
10222452 1999
8
3-Phosphoglycerate dehydrogenase deficiency and 3-phosphoserine phosphatase deficiency: inborn errors of serine biosynthesis. 61
8739971 1996

Variations for Phosphoserine Phosphatase Deficiency

ClinVar genetic disease variations for Phosphoserine Phosphatase Deficiency:

6 (show top 50) (show all 77)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 PSPH NM_004577.4(PSPH):c.155T>C (p.Met52Thr) SNV Pathogenic 13624 rs104894036 GRCh37: 7:56087413-56087413
GRCh38: 7:56019720-56019720
2 PSPH NM_004577.4(PSPH):c.103G>A (p.Ala35Thr) SNV Pathogenic 189253 rs786204793 GRCh37: 7:56088803-56088803
GRCh38: 7:56021110-56021110
3 PSPH NM_004577.4(PSPH):c.340del (p.Ser114fs) Deletion Likely pathogenic 993024 GRCh37: 7:56085008-56085008
GRCh38: 7:56017315-56017315
4 PSPH NM_004577.4(PSPH):c.455C>T (p.Thr152Ile) SNV Conflicting interpretations of pathogenicity 360505 rs147304638 GRCh37: 7:56082831-56082831
GRCh38: 7:56015138-56015138
5 PSPH NM_004577.4(PSPH):c.-228C>G SNV Uncertain significance 360522 rs886062391 GRCh37: 7:56101736-56101736
GRCh38: 7:56034043-56034043
6 PSPH NM_004577.4(PSPH):c.149G>A (p.Arg50Gln) SNV Uncertain significance 360508 rs554689284 GRCh37: 7:56087419-56087419
GRCh38: 7:56019726-56019726
7 PSPH NM_004577.4(PSPH):c.-357C>T SNV Uncertain significance 360525 rs745752622 GRCh37: 7:56118896-56118896
GRCh38: 7:56051203-56051203
8 PSPH NM_004577.4(PSPH):c.*233dup Duplication Uncertain significance 360503 rs34727399 GRCh37: 7:56079221-56079222
GRCh38: 7:56011528-56011529
9 PSPH NM_004577.4(PSPH):c.*277G>A SNV Uncertain significance 360502 rs886062389 GRCh37: 7:56079178-56079178
GRCh38: 7:56011485-56011485
10 PSPH NM_004577.4(PSPH):c.129G>A (p.Ala43=) SNV Uncertain significance 360511 rs548513131 GRCh37: 7:56088777-56088777
GRCh38: 7:56021084-56021084
11 PSPH NM_004577.4(PSPH):c.-519C>G SNV Uncertain significance 360531 rs886062395 GRCh37: 7:56119058-56119058
GRCh38: 7:56051365-56051365
12 PSPH NM_004577.4(PSPH):c.-145-15A>G SNV Uncertain significance 360520 rs552907219 GRCh37: 7:56099762-56099762
GRCh38: 7:56032069-56032069
13 PSPH NM_004577.4(PSPH):c.-333C>T SNV Uncertain significance 360523 rs886062392 GRCh37: 7:56118872-56118872
GRCh38: 7:56051179-56051179
14 PSPH NM_004577.4(PSPH):c.*316C>T SNV Uncertain significance 360500 rs190483183 GRCh37: 7:56079139-56079139
GRCh38: 7:56011446-56011446
15 PSPH NM_004577.4(PSPH):c.60T>C (p.Asp20=) SNV Uncertain significance 360517 rs201376678 GRCh37: 7:56088846-56088846
GRCh38: 7:56021153-56021153
16 PSPH NM_004577.4(PSPH):c.-430T>G SNV Uncertain significance 360526 rs886062393 GRCh37: 7:56118969-56118969
GRCh38: 7:56051276-56051276
17 PSPH NM_004577.4(PSPH):c.-461A>G SNV Uncertain significance 360529 rs886062394 GRCh37: 7:56119000-56119000
GRCh38: 7:56051307-56051307
18 PSPH NM_004577.4(PSPH):c.-339T>C SNV Uncertain significance 360524 rs535243315 GRCh37: 7:56118878-56118878
GRCh38: 7:56051185-56051185
19 PSPH NM_004577.4(PSPH):c.*341G>A SNV Uncertain significance 360498 rs886062387 GRCh37: 7:56079114-56079114
GRCh38: 7:56011421-56011421
20 PSPH NM_004577.4(PSPH):c.*309A>G SNV Uncertain significance 360501 rs886062388 GRCh37: 7:56079146-56079146
GRCh38: 7:56011453-56011453
21 PSPH NM_004577.4(PSPH):c.-235_-213delinsC Indel Uncertain significance 360521 rs886062390 GRCh37: 7:56101721-56101743
GRCh38: 7:56034028-56034050
22 PSPH NM_004577.4(PSPH):c.-485A>G SNV Uncertain significance 360530 rs530804173 GRCh37: 7:56119024-56119024
GRCh38: 7:56051331-56051331
23 PSPH NM_004577.3(PSPH):c.-681A>C SNV Uncertain significance 360533 rs886062396 GRCh37: 7:56119220-56119220
GRCh38: 7:56051527-56051527
24 PSPH NM_004577.3(PSPH):c.-720G>T SNV Uncertain significance 360539 rs190794562 GRCh37: 7:56119259-56119259
GRCh38: 7:56051566-56051566
25 PSPH NM_004577.3(PSPH):c.-708C>A SNV Uncertain significance 360536 rs187219685 GRCh37: 7:56119247-56119247
GRCh38: 7:56051554-56051554
26 PSPH NM_004577.3(PSPH):c.-683G>C SNV Uncertain significance 360534 rs148855313 GRCh37: 7:56119222-56119222
GRCh38: 7:56051529-56051529
27 PSPH NM_004577.3(PSPH):c.-711G>A SNV Uncertain significance 360537 rs886062397 GRCh37: 7:56119250-56119250
GRCh38: 7:56051557-56051557
28 PSPH NM_004577.3(PSPH):c.-708C>G SNV Uncertain significance 360535 rs187219685 GRCh37: 7:56119247-56119247
GRCh38: 7:56051554-56051554
29 PSPH NM_004577.3(PSPH):c.-715T>C SNV Uncertain significance 360538 rs886062398 GRCh37: 7:56119254-56119254
GRCh38: 7:56051561-56051561
30 PSPH NM_004577.4(PSPH):c.481G>A (p.Val161Met) SNV Uncertain significance 910293 GRCh37: 7:56082805-56082805
GRCh38: 7:56015112-56015112
31 PSPH NM_004577.4(PSPH):c.235C>T (p.Leu79Phe) SNV Uncertain significance 910294 GRCh37: 7:56087333-56087333
GRCh38: 7:56019640-56019640
32 PSPH NM_004577.4(PSPH):c.-396C>G SNV Uncertain significance 910354 GRCh37: 7:56118935-56118935
GRCh38: 7:56051242-56051242
33 PSPH NM_004577.4(PSPH):c.*588G>A SNV Uncertain significance 911456 GRCh37: 7:56078867-56078867
GRCh38: 7:56011174-56011174
34 PSPH NM_004577.4(PSPH):c.115G>A (p.Gly39Ser) SNV Uncertain significance 908538 GRCh37: 7:56088791-56088791
GRCh38: 7:56021098-56021098
35 PSPH NM_004577.4(PSPH):c.*278C>T SNV Uncertain significance 909321 GRCh37: 7:56079177-56079177
GRCh38: 7:56011484-56011484
36 PSPH NM_004577.4(PSPH):c.*203T>C SNV Uncertain significance 909322 GRCh37: 7:56079252-56079252
GRCh38: 7:56011559-56011559
37 PSPH NM_004577.4(PSPH):c.*157C>T SNV Uncertain significance 909323 GRCh37: 7:56079298-56079298
GRCh38: 7:56011605-56011605
38 PSPH NM_004577.4(PSPH):c.*46A>C SNV Uncertain significance 909324 GRCh37: 7:56079409-56079409
GRCh38: 7:56011716-56011716
39 PSPH NM_004577.4(PSPH):c.*22A>G SNV Uncertain significance 909325 GRCh37: 7:56079433-56079433
GRCh38: 7:56011740-56011740
40 PSPH NM_004577.4(PSPH):c.*12G>A SNV Uncertain significance 909326 GRCh37: 7:56079443-56079443
GRCh38: 7:56011750-56011750
41 PSPH NM_004577.4(PSPH):c.-130G>T SNV Uncertain significance 360519 rs529188025 GRCh37: 7:56099732-56099732
GRCh38: 7:56032039-56032039
42 PSPH NM_004577.4(PSPH):c.*371A>G SNV Uncertain significance 360496 rs564916020 GRCh37: 7:56079084-56079084
GRCh38: 7:56011391-56011391
43 PSPH NM_004577.4(PSPH):c.*649A>C SNV Uncertain significance 360493 rs766855269 GRCh37: 7:56078806-56078806
GRCh38: 7:56011113-56011113
44 PSPH NM_004577.4(PSPH):c.*457C>T SNV Uncertain significance 908474 GRCh37: 7:56078998-56078998
GRCh38: 7:56011305-56011305
45 PSPH NM_004577.4(PSPH):c.-22A>G SNV Uncertain significance 909403 GRCh37: 7:56099624-56099624
GRCh38: 7:56031931-56031931
46 PSPH NM_004577.4(PSPH):c.-94G>A SNV Uncertain significance 909404 GRCh37: 7:56099696-56099696
GRCh38: 7:56032003-56032003
47 PSPH NM_004577.4(PSPH):c.596A>T (p.Asn199Ile) SNV Uncertain significance 944490 GRCh37: 7:56079537-56079537
GRCh38: 7:56011844-56011844
48 PSPH NM_004577.4(PSPH):c.673G>C (p.Glu225Gln) SNV Uncertain significance 999748 GRCh37: 7:56079460-56079460
GRCh38: 7:56011767-56011767
49 PSPH NM_004577.4(PSPH):c.94G>A (p.Asp32Asn) SNV Uncertain significance 13623 rs104894035 GRCh37: 7:56088812-56088812
GRCh38: 7:56021119-56021119
50 PSPH NM_004577.4(PSPH):c.72G>C (p.Thr24=) SNV Likely benign 360516 rs145408555 GRCh37: 7:56088834-56088834
GRCh38: 7:56021141-56021141

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

72
# Symbol AA change Variation ID SNP ID
1 PSPH p.Asp32Asn VAR_022378 rs104894035
2 PSPH p.Met52Thr VAR_022379 rs104894036

Expression for Phosphoserine Phosphatase Deficiency

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

Pathways for Phosphoserine Phosphatase Deficiency

Pathways related to Phosphoserine Phosphatase Deficiency according to KEGG:

36
# Name Kegg Source Accession
1 Glycine, serine and threonine metabolism hsa00260

GO Terms for Phosphoserine Phosphatase Deficiency

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

# Name GO ID Score Top Affiliating Genes
1 cellular amino acid biosynthetic process GO:0008652 9.16 PSPH PHGDH
2 L-serine biosynthetic process GO:0006564 8.96 PSPH PHGDH
3 L-serine metabolic process GO:0006563 8.62 PSPH PHGDH

Sources for Phosphoserine Phosphatase 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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