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Aliases for PSPH Gene

Aliases for PSPH Gene

  • Phosphoserine Phosphatase 2 3 5
  • O-Phosphoserine Phosphohydrolase 3 4
  • L-3-Phosphoserine Phosphatase 3 4
  • EC 3.1.3.3 4 56
  • PSPase 3 4
  • PSP 3 4
  • PSPHD 3

External Ids for PSPH Gene

Previous HGNC Symbols for PSPH Gene

  • PSP

Previous GeneCards Identifiers for PSPH Gene

  • GC07M055542
  • GC07M055785
  • GC07M055820
  • GC07M055853
  • GC07M055892

Summaries for PSPH Gene

Entrez Gene Summary for PSPH Gene

  • 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]

GeneCards Summary for PSPH Gene

PSPH (Phosphoserine Phosphatase) is a Protein Coding gene. Diseases associated with PSPH include Phosphoserine Phosphatase Deficiency and Serine Deficiency. Among its related pathways are Viral mRNA Translation and Metabolism. Gene Ontology (GO) annotations related to this gene include calcium ion binding and magnesium ion binding.

UniProtKB/Swiss-Prot for PSPH Gene

  • Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.

Gene Wiki entry for PSPH Gene

Additional gene information for PSPH Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PSPH Gene

Genomics for PSPH Gene

GeneHancer (GH) Regulatory Elements for PSPH Gene

Promoters and enhancers for PSPH Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I056031 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 550.4 +18.4 18382 4 PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF213 ZNF143 PSPH SUMF2 NIPSNAP2 PSPHP1 ZNF713 PIR39528
GH07I056049 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 556.9 -0.4 -423 4.3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ZNF207 PSPH CCT6A CHCHD2 SUMF2 NIPSNAP2 LOC154937 PSPHP1 PIR60303 GC07P056054
GH07I056059 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 6.2 -11.1 -11080 6.2 HDGF SMAD1 ARID4B SIN3A DMAP1 YY1 POLR2B E2F8 ZNF143 FOS SUMF2 NIPSNAP2 CHCHD2 PHKG1 PSPHP1 MRPS17 PSPH GC07P056082 SNORA15 CCT6A
GH07I056046 Enhancer 0.8 ENCODE 7 +4.0 4003 2.9 ZNF2 YY1 ZNF335 ZNF362 ZNF398 NR2F2 SP1 NFIC RCOR2 IKZF1 CHCHD2 PSPH PIR39528
GH07I056004 Enhancer 1.2 Ensembl ENCODE 0.3 +43.9 43898 6.8 FOXA2 MLX ARNT ARID4B DMAP1 ZNF2 ZNF48 ETS1 TCF12 SLC30A9 NIPSNAP2 SUMF2 CCT6A PHKG1 LOC154937 MRPS17 PSPHP1 ZNF713 NUPR2 PIR39528
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PSPH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PSPH gene promoter:

Genomic Locations for PSPH Gene

Genomic Locations for PSPH Gene
chr7:56,010,363-56,051,604
(GRCh38/hg38)
Size:
41,242 bases
Orientation:
Minus strand
chr7:56,078,744-56,119,297
(GRCh37/hg19)

Genomic View for PSPH Gene

Genes around PSPH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PSPH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PSPH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PSPH Gene

Proteins for PSPH Gene

  • Protein details for PSPH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78330-SERB_HUMAN
    Recommended name:
    Phosphoserine phosphatase
    Protein Accession:
    P78330
    Secondary Accessions:
    • B2RCR5
    • Q7Z3S5

    Protein attributes for PSPH Gene

    Size:
    225 amino acids
    Molecular mass:
    25008 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PSPH Gene

neXtProt entry for PSPH Gene

Selected DME Specific Peptides for PSPH Gene

P78330:
  • TNVFANRLKFYFNGEYAGFDE
  • WYITDFVELLG
  • FIGFGGNV
  • RLALIQPSR
  • QPTAESGGKGKVI

Post-translational modifications for PSPH Gene

No Post-translational modifications

Domains & Families for PSPH Gene

Gene Families for PSPH Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PSPH Gene

Suggested Antigen Peptide Sequences for PSPH Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P78330

UniProtKB/Swiss-Prot:

SERB_HUMAN :
  • Belongs to the HAD-like hydrolase superfamily. SerB family.
Family:
  • Belongs to the HAD-like hydrolase superfamily. SerB family.
genes like me logo Genes that share domains with PSPH: view

Function for PSPH Gene

Molecular function for PSPH Gene

GENATLAS Biochemistry:
phosphoserine phosphatase,catalyzing the last step of serine biosynthesis
UniProtKB/Swiss-Prot CatalyticActivity:
O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by calcium ions.
UniProtKB/Swiss-Prot Function:
Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.

Enzyme Numbers (IUBMB) for PSPH Gene

Phenotypes From GWAS Catalog for PSPH Gene

Gene Ontology (GO) - Molecular Function for PSPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IDA 15291819
GO:0004647 phosphoserine phosphatase activity TAS,IEA --
GO:0005509 calcium ion binding IDA 12777757
GO:0016787 hydrolase activity IEA --
GO:0042803 protein homodimerization activity IPI 12777757
genes like me logo Genes that share ontologies with PSPH: view
genes like me logo Genes that share phenotypes with PSPH: view

Human Phenotype Ontology for PSPH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PSPH Gene

MGI Knock Outs for PSPH:
  • Psph tm1a(EUCOMM)Hmgu
  • Psph tm1.1(KOMP)Vlcg

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for PSPH Gene

Localization for PSPH Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PSPH gene
Compartment Confidence
cytosol 5
cytoskeleton 3
plasma membrane 1
mitochondrion 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PSPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0043005 neuron projection IEA --
genes like me logo Genes that share ontologies with PSPH: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PSPH Gene

Pathways & Interactions for PSPH Gene

genes like me logo Genes that share pathways with PSPH: view

UniProtKB/Swiss-Prot P78330-SERB_HUMAN

  • Pathway: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 3/3.

Gene Ontology (GO) - Biological Process for PSPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006563 L-serine metabolic process IDA,TAS 15291819
GO:0006564 L-serine biosynthetic process TAS,IEA --
GO:0008652 cellular amino acid biosynthetic process IEA --
GO:0009612 response to mechanical stimulus IEA --
GO:0016311 dephosphorylation IEA --
genes like me logo Genes that share ontologies with PSPH: view

No data available for SIGNOR curated interactions for PSPH Gene

Drugs & Compounds for PSPH Gene

(13) Drugs for PSPH Gene - From: DrugBank, ApexBio, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Zinc Approved, Investigational Pharma Target 2430
D-serine Approved, Experimental, Investigational Pharma Agonist 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Magnesium Approved Nutra 0

(4) Additional Compounds for PSPH Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
DL-O-Phosphoserine
  • 3-Phospho-1-serine
  • 3-Phospho-serine
  • 3-Phosphoserine
  • DL-O-Phosphorylserine
  • DL-O-Phosphoserine
17885-08-4
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2

(1) ApexBio Compounds for PSPH Gene

Compound Action Cas Number
DL-AP3 Glutamate receptor antagonist and HPSP inhibitor 20263-06-3
genes like me logo Genes that share compounds with PSPH: view

Drug Products

Transcripts for PSPH Gene

Unigene Clusters for PSPH Gene

Phosphoserine phosphatase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PSPH Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g · 1h ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d · 7e · 7f ^ 8 ^ 9 ^ 10 ^ 11a · 11b ·
SP1: - - -
SP2: - - - - - - - - -
SP3: -
SP4: -
SP5: - -
SP6: -
SP7: - - - - - - - - -
SP8:
SP9: - - - - - - - - - - -
SP10: - - - - - - - - - -
SP11: - - - - - - - - - - -
SP12: - - - - - - - - -
SP13: - - - - - - - - - -
SP14: - - - - - - - - -
SP15: - - - - - - - - -
SP16: - - - - - - - - -
SP17: - - - - - - - - - - - - - -
SP18: - - - - - - - -
SP19: - - - - -
SP20:
SP21: - - - - - - -
SP22: - - - - - - - - -
SP23: - - - - - - - - - -
SP24:
SP25: -

ExUns: 11c · 11d · 11e ^ 12a · 12b · 12c · 12d ^ 13a · 13b ^ 14 ^ 15a · 15b
SP1: -
SP2: -
SP3:
SP4: -
SP5: -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17: -
SP18:
SP19: - - - - - - - - -
SP20:
SP21:
SP22:
SP23:
SP24:
SP25:

Relevant External Links for PSPH Gene

GeneLoc Exon Structure for
PSPH
ECgene alternative splicing isoforms for
PSPH

Expression for PSPH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PSPH Gene

Protein differential expression in normal tissues from HIPED for PSPH Gene

This gene is overexpressed in Fetal gut (11.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PSPH Gene



Protein tissue co-expression partners for PSPH Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PSPH Gene:

PSPH

SOURCE GeneReport for Unigene cluster for PSPH Gene:

Hs.512656

Evidence on tissue expression from TISSUES for PSPH Gene

  • Kidney(4.3)
  • Nervous system(3.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PSPH Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
Regions:
Head and neck:
  • brain
  • head
genes like me logo Genes that share expression patterns with PSPH: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PSPH Gene

Orthologs for PSPH Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PSPH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PSPH 33 34
  • 99.7 (n)
dog
(Canis familiaris)
Mammalia PSPH 33 34
  • 91.26 (n)
cow
(Bos Taurus)
Mammalia PSPH 33 34
  • 90.96 (n)
oppossum
(Monodelphis domestica)
Mammalia PSPH 34
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Psph 33 16 34
  • 86.96 (n)
rat
(Rattus norvegicus)
Mammalia Psph 33
  • 86.52 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PSPH 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves PSPH 33 34
  • 73.63 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia psph 33
  • 74.11 (n)
Str.15388 33
zebrafish
(Danio rerio)
Actinopterygii psph 33 34
  • 64.89 (n)
fruit fly
(Drosophila melanogaster)
Insecta aay 33 34
  • 55.61 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012247 33
  • 53.86 (n)
worm
(Caenorhabditis elegans)
Secernentea Y62E10A.13 33 34
  • 55 (n)
Y62E10A.13a 35
  • 50 (a)
Y62E10A.13b 35
  • 50 (a)
Y62E10A.13c 35
  • 49 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SER2 34 36
  • 19 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons PSP 33
  • 53.72 (n)
rice
(Oryza sativa)
Liliopsida Os12g0502400 33
  • 56.65 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1610 33
Species where no ortholog for PSPH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PSPH Gene

ENSEMBL:
Gene Tree for PSPH (if available)
TreeFam:
Gene Tree for PSPH (if available)

Paralogs for PSPH Gene

(1) SIMAP similar genes for PSPH Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for PSPH Gene

genes like me logo Genes that share paralogs with PSPH: view

No data available for Paralogs for PSPH Gene

Variants for PSPH Gene

Sequence variations from dbSNP and Humsavar for PSPH Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs104894035 pathogenic, Deficiency of phosphoserine phosphatase, Phosphoserine phosphatase deficiency (PSPHD) [MIM:614023] 56,021,119(-) C/T coding_sequence_variant, missense_variant
rs104894036 pathogenic, Deficiency of phosphoserine phosphatase, Phosphoserine phosphatase deficiency (PSPHD) [MIM:614023] 56,019,720(-) A/G coding_sequence_variant, intron_variant, missense_variant
rs144281276 uncertain-significance, Deficiency of phosphoserine phosphatase 56,019,729(-) C/T coding_sequence_variant, intron_variant, missense_variant
rs145408555 uncertain-significance, Deficiency of phosphoserine phosphatase 56,021,141(-) C/G/T coding_sequence_variant, synonymous_variant
rs145544909 likely-benign, Deficiency of phosphoserine phosphatase 56,011,356(-) C/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PSPH Gene

Variant ID Type Subtype PubMed ID
nsv970838 CNV duplication 23825009
nsv824122 CNV gain 20364138
nsv819501 CNV gain 19587683
nsv1137223 CNV deletion 24896259
nsv1019400 CNV gain 25217958
nsv1017793 CNV gain 25217958
esv3613259 CNV gain 21293372
esv3613258 CNV gain 21293372
esv3613248 CNV gain 21293372
esv3576357 CNV gain 25503493
esv28230 CNV gain+loss 19812545
esv2761334 CNV gain 21179565
esv2734448 CNV deletion 23290073
esv2734447 CNV deletion 23290073
esv1571450 CNV insertion 17803354
dgv6362n100 CNV gain 25217958
dgv1201e199 CNV deletion 23128226
dgv1107n67 CNV gain 20364138
dgv1106n67 CNV gain 20364138

Variation tolerance for PSPH Gene

Residual Variation Intolerance Score: 90.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.35; 26.79% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PSPH Gene

Human Gene Mutation Database (HGMD)
PSPH
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PSPH

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PSPH Gene

Disorders for PSPH Gene

MalaCards: The human disease database

(6) MalaCards diseases for PSPH Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
phosphoserine phosphatase deficiency
  • psphd
serine deficiency
phosphoserine aminotransferase deficiency
  • psatd
lacrimal gland adenocarcinoma
  • adenocarcinoma of lacrimal gland
lacrimal gland carcinoma
  • carcinoma of the lacrimal gland
- elite association - COSMIC cancer census association via MalaCards
Search PSPH in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SERB_HUMAN
  • Phosphoserine phosphatase deficiency (PSPHD) [MIM:614023]: A disorder that results in pre- and postnatal growth retardation, moderate psychomotor retardation and facial features suggestive of Williams syndrome. {ECO:0000269 PubMed:14673469}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PSPH

genes like me logo Genes that share disorders with PSPH: view

No data available for Genatlas for PSPH Gene

Publications for PSPH Gene

  1. High-resolution structure of human phosphoserine phosphatase in open conformation. (PMID: 12777757) Peeraer Y … De Ranter C (Acta crystallographica. Section D, Biological crystallography 2003) 3 4 22 58
  2. Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase. (PMID: 12213811) Kim HY … Hwang KY (The Journal of biological chemistry 2002) 3 4 22 58
  3. Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate. (PMID: 9188776) Collet JF … Van Schaftingen E (FEBS letters 1997) 2 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for PSPH Gene

Sources for PSPH Gene

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