Gene Gene information from NCBI Gene database.
Entrez ID 5723
Gene name Phosphoserine phosphatase
Gene symbol PSPH
Synonyms (NCBI Gene)
PSPPSPHD
Chromosome 7
Chromosome location 7p11.2
Summary The protein encoded by this gene belongs to a subfamily of the phosphotransferases. This encoded enzyme is responsible for the third and last step in L-serine formation. It catalyzes magnesium-dependent hydrolysis of L-phosphoserine and is also involved i
SNPs SNP information provided by dbSNP.
4
SNP ID Visualize variation Clinical significance Consequence
rs73343752 A>G Likely-benign, conflicting-interpretations-of-pathogenicity Missense variant, non coding transcript variant, coding sequence variant
rs104894035 C>T Pathogenic Non coding transcript variant, missense variant, coding sequence variant
rs104894036 A>G Pathogenic Non coding transcript variant, intron variant, coding sequence variant, missense variant
rs786204793 C>T Pathogenic Coding sequence variant, non coding transcript variant, missense variant
miRNA miRNA information provided by mirtarbase database.
389
miRTarBase ID miRNA Experiments Reference
MIRT023338 hsa-miR-122-5p Proteomics 21750653
MIRT032012 hsa-miR-16-5p Proteomics 18668040
MIRT038375 hsa-miR-296-3p CLASH 23622248
MIRT654660 hsa-miR-3163 HITS-CLIP 23824327
MIRT654659 hsa-miR-4729 HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
24
GO ID Ontology Definition Evidence Reference
GO:0000287 Function Magnesium ion binding IBA
GO:0000287 Function Magnesium ion binding IDA 15291819
GO:0001701 Process In utero embryonic development IEA
GO:0005737 Component Cytoplasm IBA
GO:0005737 Component Cytoplasm IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
172480 9577 ENSG00000146733
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P78330
Protein name Phosphoserine phosphatase (PSP) (PSPase) (EC 3.1.3.3) (L-3-phosphoserine phosphatase) (O-phosphoserine phosphohydrolase)
Protein function Catalyzes the last irreversible step in the biosynthesis of L-serine from carbohydrates, the dephosphorylation of O-phospho-L-serine to L-serine (PubMed:12213811, PubMed:14673469, PubMed:15291819, PubMed:25080166, PubMed:9222972). L-serine can t
PDB 1L8L , 1L8O , 1NNL , 6HYJ , 6HYY , 6Q6J
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00702 Hydrolase 14 191 Domain
Sequence
Sequence length 225
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Glycine, serine and threonine metabolism
Metabolic pathways
Carbon metabolism
Biosynthesis of amino acids
  Serine biosynthesis
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
33
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Deficiency of phosphoserine phosphatase Pathogenic; Likely pathogenic rs786204793, rs104894036, rs1264747554, rs1788688718 RCV000169687
RCV000014594
RCV004799409
RCV001283838
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Amelogenesis imperfecta Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AMINO ACID METABOLISM, INBORN ERRORS CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
3-phosphoserine phosphatase deficiency, infantile/juvenile form 3-phosphoserine phosphatase deficiency Orphanet
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 15154633
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of prostate Prostate adenocarcinoma BEFREE 15727931
★☆☆☆☆
Found in Text Mining only
Amino Acid Metabolism, Inborn Errors Disorder of amino acid metabolism CTD_human_DG 14673469
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Amino Acid Metabolism, Inherited Disorders Inherited Errors of Amino Acid Metabolism CTD_human_DG 14673469
★☆☆☆☆
Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA Syndromic microphthalmia BEFREE 24069258
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder BEFREE 29419656
★☆☆☆☆
Found in Text Mining only
Anxiety Disorders Anxiety Disorder BEFREE 29419656
★☆☆☆☆
Found in Text Mining only
Attention Deficit Disorder Attention Deficit Hyperactivity Disorder BEFREE 10532621
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder BEFREE 10532621
★☆☆☆☆
Found in Text Mining only