MCID: PHS022
MIFTS: 30

Phosphoserine Phosphatase Deficiency

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

Aliases & Classifications for Phosphoserine Phosphatase Deficiency

MalaCards integrated aliases for Phosphoserine Phosphatase Deficiency:

Name: Phosphoserine Phosphatase Deficiency 57 12 75 13
Deficiency of Phosphoserine Phosphatase 29 6 73
Psphd 57 12 75
Psph Deficiency 12 15
3-Phosphoserine Phosphatase Deficiency 59
Deficiency, Phosphoserine Phosphatase 40
Phosphoserine Phosphatase 13

Characteristics:

Orphanet epidemiological data:

59
3-phosphoserine phosphatase deficiency
Inheritance: Autosomal recessive;

OMIM:

57
Inheritance:
autosomal recessive

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


HPO:

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


Classifications:



Summaries for Phosphoserine Phosphatase Deficiency

UniProtKB/Swiss-Prot : 75 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.

MalaCards based summary : Phosphoserine Phosphatase Deficiency, also known as deficiency of phosphoserine phosphatase, is related to hepatic encephalopathy and colorectal cancer, and has symptoms including seizures An important gene associated with Phosphoserine Phosphatase Deficiency is PSPH (Phosphoserine Phosphatase), and among its related pathways/superpathways are Carbon metabolism and One carbon pool by folate. Related phenotypes are microcephaly and intellectual disability

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

Wikipedia : 76 Phosphoserine phosphatase is an enzyme that in humans is encoded by the PSPH... more...

Description from OMIM: 614023

Related Diseases for Phosphoserine Phosphatase Deficiency

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

# Related Disease Score Top Affiliating Genes
1 hepatic encephalopathy 10.2
2 colorectal cancer 10.1
3 williams-beuren syndrome 10.0
4 phosphoserine aminotransferase deficiency 8.9 PHGDH PSPH
5 serine deficiency 8.5 ELN PHGDH PSPH

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



Diseases related to Phosphoserine Phosphatase Deficiency

Symptoms & Phenotypes for Phosphoserine Phosphatase Deficiency

Symptoms via clinical synopsis from OMIM:

57
Growth Other:
poor growth (1 patient)

Neurologic Central Nervous System:
delayed development
mental retardation
seizures
hypertonia
cerebral atrophy (rare)

Head And Neck Head:
microcephaly (rare)

Laboratory Abnormalities:
decreased plasma serine
decreased plasma glycine


Clinical features from OMIM:

614023

Human phenotypes related to Phosphoserine Phosphatase Deficiency:

32 (show all 8)
# Description HPO Frequency HPO Source Accession
1 microcephaly 32 occasional (7.5%) HP:0000252
2 intellectual disability 32 HP:0001249
3 seizures 32 HP:0001250
4 global developmental delay 32 HP:0001263
5 hypertonia 32 HP:0001276
6 intrauterine growth retardation 32 HP:0001511
7 cerebral atrophy 32 occasional (7.5%) HP:0002059
8 postnatal growth retardation 32 HP:0008897

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 Year
1
Novel Report of Phosphoserine Phosphatase Deficiency in an Adult with Myeloneuropathy and Limb Contractures. ( 26589312 )
2015
2
Phosphoserine phosphatase deficiency in a patient with Williams syndrome. ( 9222972 )
1997

Variations for Phosphoserine Phosphatase Deficiency

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

75
# Symbol AA change Variation ID SNP ID
1 PSPH p.Asp32Asn VAR_022378 rs104894035
2 PSPH p.Met52Thr VAR_022379 rs104894036

ClinVar genetic disease variations for Phosphoserine Phosphatase Deficiency:

6
(show top 50) (show all 102)
# Gene Variation Type Significance SNP ID Assembly Location
1 PSPH NM_004577.3(PSPH): c.94G> A (p.Asp32Asn) single nucleotide variant Pathogenic rs104894035 GRCh37 Chromosome 7, 56088812: 56088812
2 PSPH NM_004577.3(PSPH): c.94G> A (p.Asp32Asn) single nucleotide variant Pathogenic rs104894035 GRCh38 Chromosome 7, 56021119: 56021119
3 PSPH NM_004577.3(PSPH): c.155T> C (p.Met52Thr) single nucleotide variant Pathogenic rs104894036 GRCh37 Chromosome 7, 56087413: 56087413
4 PSPH NM_004577.3(PSPH): c.155T> C (p.Met52Thr) single nucleotide variant Pathogenic rs104894036 GRCh38 Chromosome 7, 56019720: 56019720
5 PSPH NM_004577.3(PSPH): c.103G> A (p.Ala35Thr) single nucleotide variant Pathogenic rs786204793 GRCh37 Chromosome 7, 56088803: 56088803
6 PSPH NM_004577.3(PSPH): c.103G> A (p.Ala35Thr) single nucleotide variant Pathogenic rs786204793 GRCh38 Chromosome 7, 56021110: 56021110
7 PSPH NM_004577.3(PSPH): c.146G> A (p.Arg49Gln) single nucleotide variant Uncertain significance rs144281276 GRCh37 Chromosome 7, 56087422: 56087422
8 PSPH NM_004577.3(PSPH): c.146G> A (p.Arg49Gln) single nucleotide variant Uncertain significance rs144281276 GRCh38 Chromosome 7, 56019729: 56019729
9 PSPH NM_004577.3(PSPH): c.145C> T (p.Arg49Trp) single nucleotide variant Benign rs79451216 GRCh37 Chromosome 7, 56087423: 56087423
10 PSPH NM_004577.3(PSPH): c.145C> T (p.Arg49Trp) single nucleotide variant Benign rs79451216 GRCh38 Chromosome 7, 56019730: 56019730
11 PSPH NM_004577.3(PSPH): c.117C> T (p.Gly39=) single nucleotide variant Benign rs199851385 GRCh37 Chromosome 7, 56088789: 56088789
12 PSPH NM_004577.3(PSPH): c.117C> T (p.Gly39=) single nucleotide variant Benign rs199851385 GRCh38 Chromosome 7, 56021096: 56021096
13 PSPH NM_004577.3(PSPH): c.-130G> T single nucleotide variant Uncertain significance rs529188025 GRCh37 Chromosome 7, 56099732: 56099732
14 PSPH NM_004577.3(PSPH): c.-130G> T single nucleotide variant Uncertain significance rs529188025 GRCh38 Chromosome 7, 56032039: 56032039
15 PSPH NM_004577.3(PSPH): c.-228C> G single nucleotide variant Uncertain significance rs886062391 GRCh37 Chromosome 7, 56101736: 56101736
16 PSPH NM_004577.3(PSPH): c.-228C> G single nucleotide variant Uncertain significance rs886062391 GRCh38 Chromosome 7, 56034043: 56034043
17 PSPH NM_004577.3(PSPH): c.-442A> G single nucleotide variant Uncertain significance rs184427284 GRCh38 Chromosome 7, 56051288: 56051288
18 PSPH NM_004577.3(PSPH): c.-442A> G single nucleotide variant Uncertain significance rs184427284 GRCh37 Chromosome 7, 56118981: 56118981
19 PSPH NM_004577.3(PSPH): c.*371A> G single nucleotide variant Uncertain significance rs564916020 GRCh37 Chromosome 7, 56079084: 56079084
20 PSPH NM_004577.3(PSPH): c.*371A> G single nucleotide variant Uncertain significance rs564916020 GRCh38 Chromosome 7, 56011391: 56011391
21 PSPH NM_004577.3(PSPH): c.*361A> G single nucleotide variant Benign rs4947534 GRCh37 Chromosome 7, 56079094: 56079094
22 PSPH NM_004577.3(PSPH): c.*361A> G single nucleotide variant Benign rs4947534 GRCh38 Chromosome 7, 56011401: 56011401
23 PSPH NM_004577.3(PSPH): c.*316C> T single nucleotide variant Uncertain significance rs190483183 GRCh37 Chromosome 7, 56079139: 56079139
24 PSPH NM_004577.3(PSPH): c.*316C> T single nucleotide variant Uncertain significance rs190483183 GRCh38 Chromosome 7, 56011446: 56011446
25 PSPH NM_004577.3(PSPH): c.249A> C (p.Gln83His) single nucleotide variant Likely benign rs73343757 GRCh37 Chromosome 7, 56087319: 56087319
26 PSPH NM_004577.3(PSPH): c.249A> C (p.Gln83His) single nucleotide variant Likely benign rs73343757 GRCh38 Chromosome 7, 56019626: 56019626
27 PSPH NM_004577.3(PSPH): c.120T> A (p.Val40=) single nucleotide variant Benign rs202027697 GRCh37 Chromosome 7, 56088786: 56088786
28 PSPH NM_004577.3(PSPH): c.120T> A (p.Val40=) single nucleotide variant Benign rs202027697 GRCh38 Chromosome 7, 56021093: 56021093
29 PSPH NM_004577.3(PSPH): c.81A> T (p.Arg27Ser) single nucleotide variant Benign rs74445297 GRCh37 Chromosome 7, 56088825: 56088825
30 PSPH NM_004577.3(PSPH): c.81A> T (p.Arg27Ser) single nucleotide variant Benign rs74445297 GRCh38 Chromosome 7, 56021132: 56021132
31 PSPH NM_004577.3(PSPH): c.-235_-213del23insC indel Uncertain significance rs886062390 GRCh37 Chromosome 7, 56101721: 56101743
32 PSPH NM_004577.3(PSPH): c.-235_-213del23insC indel Uncertain significance rs886062390 GRCh38 Chromosome 7, 56034028: 56034050
33 PSPH NM_004577.3(PSPH): c.-333C> T single nucleotide variant Uncertain significance rs886062392 GRCh37 Chromosome 7, 56118872: 56118872
34 PSPH NM_004577.3(PSPH): c.-333C> T single nucleotide variant Uncertain significance rs886062392 GRCh38 Chromosome 7, 56051179: 56051179
35 PSPH NM_004577.3(PSPH): c.-357C> T single nucleotide variant Uncertain significance rs745752622 GRCh37 Chromosome 7, 56118896: 56118896
36 PSPH NM_004577.3(PSPH): c.-357C> T single nucleotide variant Uncertain significance rs745752622 GRCh38 Chromosome 7, 56051203: 56051203
37 PSPH NM_004577.3(PSPH): c.-485A> G single nucleotide variant Uncertain significance rs530804173 GRCh38 Chromosome 7, 56051331: 56051331
38 PSPH NM_004577.3(PSPH): c.-485A> G single nucleotide variant Uncertain significance rs530804173 GRCh37 Chromosome 7, 56119024: 56119024
39 PSPH NM_004577.3(PSPH): c.-711G> A single nucleotide variant Uncertain significance rs886062397 GRCh37 Chromosome 7, 56119250: 56119250
40 PSPH NM_004577.3(PSPH): c.-711G> A single nucleotide variant Uncertain significance rs886062397 GRCh38 Chromosome 7, 56051557: 56051557
41 PSPH NM_004577.3(PSPH): c.-715T> C single nucleotide variant Uncertain significance rs886062398 GRCh37 Chromosome 7, 56119254: 56119254
42 PSPH NM_004577.3(PSPH): c.-715T> C single nucleotide variant Uncertain significance rs886062398 GRCh38 Chromosome 7, 56051561: 56051561
43 PSPH NM_004577.3(PSPH): c.*490C> T single nucleotide variant Likely benign rs71543776 GRCh37 Chromosome 7, 56078965: 56078965
44 PSPH NM_004577.3(PSPH): c.*490C> T single nucleotide variant Likely benign rs71543776 GRCh38 Chromosome 7, 56011272: 56011272
45 PSPH NM_004577.3(PSPH): c.*317G> A single nucleotide variant Uncertain significance rs565399960 GRCh38 Chromosome 7, 56011445: 56011445
46 PSPH NM_004577.3(PSPH): c.*317G> A single nucleotide variant Uncertain significance rs565399960 GRCh37 Chromosome 7, 56079138: 56079138
47 PSPH NM_004577.3(PSPH): c.*309A> G single nucleotide variant Uncertain significance rs886062388 GRCh37 Chromosome 7, 56079146: 56079146
48 PSPH NM_004577.3(PSPH): c.*309A> G single nucleotide variant Uncertain significance rs886062388 GRCh38 Chromosome 7, 56011453: 56011453
49 PSPH NM_004577.3(PSPH): c.*11C> T single nucleotide variant Likely benign rs35136814 GRCh37 Chromosome 7, 56079444: 56079444
50 PSPH NM_004577.3(PSPH): c.*11C> T single nucleotide variant Likely benign rs35136814 GRCh38 Chromosome 7, 56011751: 56011751

Expression for Phosphoserine Phosphatase Deficiency

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

Pathways for Phosphoserine Phosphatase Deficiency

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 PHGDH PSPH
2 L-serine metabolic process GO:0006563 8.96 PHGDH PSPH
3 L-serine biosynthetic process GO:0006564 8.62 PHGDH PSPH

Sources for Phosphoserine Phosphatase 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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