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PSPH phosphoserine phosphatase [ Homo sapiens (human) ]

Gene ID: 5723, updated on 10-Dec-2019

Summary

Official Symbol
PSPHprovided by HGNC
Official Full Name
phosphoserine phosphataseprovided by HGNC
Primary source
HGNC:HGNC:9577
See related
Ensembl:ENSG00000146733 MIM:172480
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PSP; PSPHD
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 in an exchange reaction between L-serine and L-phosphoserine. Deficiency of this protein is thought to be linked to Williams syndrome. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in kidney (RPKM 3.8), thyroid (RPKM 3.1) and 25 other tissues See more
Orthologs

Genomic context

See PSPH in Genome Data Viewer
Location:
7p11.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (56010487..56051604, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (56078056..56119297, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein S17 Neighboring gene nipsnap homolog 2 Neighboring gene small nucleolar RNA, H/ACA box 22B Neighboring gene chaperonin containing TCP1 subunit 6A Neighboring gene small nucleolar RNA, H/ACA box 15

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Deficiency of phosphoserine phosphatase
MedGen: C1291463 OMIM: 614023 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke.
NHGRI GWA Catalog

Pathways from BioSystems

  • Amino acid synthesis and interconversion (transamination), organism-specific biosystem (from REACTOME)
    Amino acid synthesis and interconversion (transamination), organism-specific biosystemThese reactions mediate the synthesis of aspartate, asparagine, glutamate, and glutamine from ammonia and intermediates of glycolysis, and allow the utilization of the carbon atoms from these four am...
  • Biosynthesis of amino acids, organism-specific biosystem (from KEGG)
    Biosynthesis of amino acids, organism-specific biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Biosynthesis of amino acids, conserved biosystem (from KEGG)
    Biosynthesis of amino acids, conserved biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Carbon metabolism, organism-specific biosystem (from KEGG)
    Carbon metabolism, organism-specific biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Carbon metabolism, conserved biosystem (from KEGG)
    Carbon metabolism, conserved biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Glycine, serine and threonine metabolism, organism-specific biosystem (from KEGG)
    Glycine, serine and threonine metabolism, organism-specific biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Glycine, serine and threonine metabolism, conserved biosystem (from KEGG)
    Glycine, serine and threonine metabolism, conserved biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of amino acids and derivatives, organism-specific biosystem (from REACTOME)
    Metabolism of amino acids and derivatives, organism-specific biosystemThis group of reactions is responsible for: 1) the breakdown of amino acids; 2) the synthesis of urea from ammonia and amino groups generated by amino acid breakdown; 3) the synthesis of the ten amin...
  • Serine biosynthesis, organism-specific biosystem (from REACTOME)
    Serine biosynthesis, organism-specific biosystemL-Serine is needed in human brain in large amounts as precursor to important biomolecules such as nucleotides, phospholipids and the neurotransmitters glycine and D-serine. The pathway for its synthe...
  • Serine biosynthesis, glycerate-3P => serine, organism-specific biosystem (from KEGG)
    Serine biosynthesis, glycerate-3P => serine, organism-specific biosystemPathway module; Nucleotide and amino acid metabolism; Serine and threonine metabolism
  • Serine biosynthesis, glycerate-3P => serine, conserved biosystem (from KEGG)
    Serine biosynthesis, glycerate-3P => serine, conserved biosystemPathway module; Nucleotide and amino acid metabolism; Serine and threonine metabolism
  • Trans-sulfuration and one carbon metabolism, organism-specific biosystem (from WikiPathways)
    Trans-sulfuration and one carbon metabolism, organism-specific biosystem
    Trans-sulfuration and one carbon metabolism

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
magnesium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
magnesium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphoserine phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphoserine phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
L-serine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
L-serine biosynthetic process TAS
Traceable Author Statement
more info
 
L-serine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
response to mechanical stimulus IEA
Inferred from Electronic Annotation
more info
 
response to nutrient levels IEA
Inferred from Electronic Annotation
more info
 
response to testosterone IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
neuron projection IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
phosphoserine phosphatase
Names
L-3-phosphoserine phosphatase
O-phosphoserine phosphohydrolase
PSPase
NP_001357432.1
NP_001357433.1
NP_001357434.1
NP_001357435.1
NP_001357436.1
NP_001357437.1
NP_001357438.1
NP_001357439.1
NP_001357440.1
NP_001357441.1
NP_001357442.1
NP_001357443.1
NP_001357444.1
NP_001357445.1
NP_001357446.1
NP_001357447.1
NP_001357448.1
NP_001357449.1
NP_001357450.1
NP_001357451.1
NP_004568.2
XP_006715824.1
XP_016867956.1
XP_016867957.1
XP_016867958.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011473.1 RefSeqGene

    Range
    5132..45512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001370503.1NP_001357432.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Related
    ENSP00000378854.3, ENST00000395471.7
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  2. NM_001370504.1NP_001357433.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  3. NM_001370505.1NP_001357434.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  4. NM_001370506.1NP_001357435.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  5. NM_001370507.1NP_001357436.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  6. NM_001370508.1NP_001357437.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  7. NM_001370509.1NP_001357438.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Related
    ENSP00000401639.2, ENST00000437355.6
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  8. NM_001370510.1NP_001357439.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  9. NM_001370511.1NP_001357440.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  10. NM_001370512.1NP_001357441.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Related
    ENSP00000398653.1, ENST00000421626.5
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  11. NM_001370513.1NP_001357442.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  12. NM_001370514.1NP_001357443.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  13. NM_001370515.1NP_001357444.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  14. NM_001370516.1NP_001357445.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  15. NM_001370517.1NP_001357446.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  16. NM_001370518.1NP_001357447.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  17. NM_001370519.1NP_001357448.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  18. NM_001370520.1NP_001357449.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  19. NM_001370521.1NP_001357450.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  20. NM_001370522.1NP_001357451.1  phosphoserine phosphatase

    Status: REVIEWED

    Source sequence(s)
    AC092579
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  21. NM_004577.4NP_004568.2  phosphoserine phosphatase

    See identical proteins and their annotated locations for NP_004568.2

    Status: REVIEWED

    Source sequence(s)
    AW574794, BC052958, BC063614, Y10275
    Consensus CDS
    CCDS5522.1
    UniProtKB/Swiss-Prot
    P78330
    UniProtKB/TrEMBL
    A0A024RDL3
    Related
    ENSP00000275605.3, ENST00000275605.8
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    56010487..56051604 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017012467.2XP_016867956.1  phosphoserine phosphatase isoform X1

    UniProtKB/Swiss-Prot
    P78330
    UniProtKB/TrEMBL
    A0A024RDL3
    Conserved Domains (1) summary
    cd04309
    Location:15216
    HAD_PSP_eu; phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase
  2. XM_017012469.2XP_016867958.1  phosphoserine phosphatase isoform X2

    Conserved Domains (2) summary
    pfam00702
    Location:47141
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:10179
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  3. XM_006715761.2XP_006715824.1  phosphoserine phosphatase isoform X2

    Conserved Domains (2) summary
    pfam00702
    Location:47141
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:10179
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  4. XM_017012468.2XP_016867957.1  phosphoserine phosphatase isoform X2

    Conserved Domains (2) summary
    pfam00702
    Location:47141
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:10179
    HAD_like; Haloacid Dehalogenase-like Hydrolases

RNA

  1. XR_002956470.1 RNA Sequence

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