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    PTDSS1 phosphatidylserine synthase 1 [ Homo sapiens (human) ]

    Gene ID: 9791, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PTDSS1provided by HGNC
    Official Full Name
    phosphatidylserine synthase 1provided by HGNC
    Primary source
    HGNC:HGNC:9587
    See related
    Ensembl:ENSG00000156471 MIM:612792; AllianceGenome:HGNC:9587
    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
    LMHD; PSS1; PSSA
    Summary
    The protein encoded by this gene catalyzes the formation of phosphatidylserine from either phosphatidylcholine or phosphatidylethanolamine. Phosphatidylserine localizes to the mitochondria-associated membrane of the endoplasmic reticulum, where it serves a structural role as well as a signaling role. Defects in this gene are a cause of Lenz-Majewski hyperostotic dwarfism. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2014]
    Expression
    Ubiquitous expression in heart (RPKM 35.2), placenta (RPKM 27.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    8q22.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (96261902..96336995)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (97387620..97462689)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (97274130..97349223)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27659 Neighboring gene UQCRB antisense RNA 1 Neighboring gene ubiquinol-cytochrome c reductase binding protein Neighboring gene mitochondrial transcription termination factor 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:97272591-97273284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27660 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:97273659-97273983 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:97273978-97274670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27661 Neighboring gene uncharacterized LOC105375652 Neighboring gene Sharpr-MPRA regulatory region 10382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27664 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:97339509-97340044 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:97340045-97340580 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:97351756-97352256 Neighboring gene uncharacterized LOC102724804 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:97388962-97389724 Neighboring gene uncharacterized LOC105375653 Neighboring gene RNA, U6 small nuclear 1172, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Topology of phosphatidylserine synthase 1 in the endoplasmic reticulum membrane. Miyata N, et al. Protein Sci, 2021 Nov. PMID 34516042, Free PMC Article
    2. Cutis laxa and excessive bone growth due to de novo mutations in PTDSS1. Piard J, et al. Am J Med Genet A, 2018 Mar. PMID 29341480, Free PMC Article
    3. Lenz-Majewski mutations in PTDSS1 affect phosphatidylinositol 4-phosphate metabolism at ER-PM and ER-Golgi junctions. Sohn M, et al. Proc Natl Acad Sci U S A, 2016 Apr 19. PMID 27044099, Free PMC Article
    4. Gain-of-function mutations in the phosphatidylserine synthase 1 (PTDSS1) gene cause Lenz-Majewski syndrome. Sousa SB, et al. Nat Genet, 2014 Jan. PMID 24241535
    5. A Chinese hamster cDNA encoding a protein essential for phosphatidylserine synthase I activity. Kuge O, et al. J Biol Chem, 1991 Dec 15. PMID 1748687

    See all (69) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Disease-related PSS1 mutant impedes the formation and function of osteoclasts.
      Title: Disease-related PSS1 mutant impedes the formation and function of osteoclasts.
    2. Topology of phosphatidylserine synthase 1 in the endoplasmic reticulum membrane.
      Title: Topology of phosphatidylserine synthase 1 in the endoplasmic reticulum membrane.
    3. used transpose-mediated transgenesis to attempt to stably express wild-type and mutant forms of human PTDSS1 ubiquitously or specifically in chondrocytes, osteoblasts or osteoclasts in zebrafish
      Title: Analysis of transgenic zebrafish expressing the Lenz-Majewski syndrome gene PTDSS1 in skeletal cell lineages.
    4. we report here three patients with LMS and heterozygous mutations in PTDSS1. We describe an adult phenotype and two novel PTDSS1 mutations. We suggest that LMS should be considered in the differential diagnosis of a newborn with CL.
      Title: Cutis laxa and excessive bone growth due to de novo mutations in PTDSS1.
    5. RYR2, PTDSS1 and AREG are autism susceptibility genes that are implicated in a Lebanese population-based study of copy number variations in this disease.
      Title: RYR2, PTDSS1 and AREG genes are implicated in a Lebanese population-based study of copy number variation in autism.
    6. PSS1 mutations not only affect cellular PS levels and distribution but also lead to a more complex imbalance in lipid homeostasis by disturbing PI4P metabolism.
      Title: Lenz-Majewski mutations in PTDSS1 affect phosphatidylinositol 4-phosphate metabolism at ER-PM and ER-Golgi junctions.
    7. Gain-of-function missense mutations in the phosphatidylserine synthase 1 (PTDSS1) gene cause Lenz-Majewski syndrome.
      Title: Gain-of-function mutations in the phosphatidylserine synthase 1 (PTDSS1) gene cause Lenz-Majewski syndrome.
    8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    9. Purification and characterization of human phosphatidylserine synthases 1 and 2.
      Title: Purification and characterization of human phosphatidylserine synthases 1 and 2.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Lenz-Majewski hyperostosis syndrome
    MedGen: C0432269 OMIM: 151050 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of phosphatidylserine synthase 1 (PTDSS1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify phosphatidylserine synthase 1 (PTDSS1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify phosphatidylserine synthase 1 (PTDSS1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify phosphatidylserine synthase 1 (PTDSS1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify phosphatidylserine synthase 1 (PTDSS1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0024

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-serine-phosphatidylcholine phosphatidyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables L-serine-phosphatidylcholine phosphatidyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables L-serine-phosphatidylethanolamine phosphatidyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables L-serine-phosphatidylethanolamine phosphatidyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables transferase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in phosphatidylserine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphatidylserine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylserine biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    phosphatidylserine synthase 1
    Names
    PSS-1
    ptdSer synthase 1
    serine-exchange enzyme I
    NP_001277154.1
    NP_055569.1

    NCBI Reference Sequences (RefSeq)

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    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_034054.2 RefSeqGene

      Range
      5002..80095
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001290225.2 → NP_001277154.1  phosphatidylserine synthase 1 isoform 2

      See identical proteins and their annotated locations for NP_001277154.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two consecutive alternate exons compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AP003465, BC002376, BM459031, HY087183
      UniProtKB/TrEMBL
      Q9BSY0
      Conserved Domains (1) summary
      pfam03034
      Location:1 → 225
      PSS; Phosphatidyl serine synthase

    2. NM_014754.3 → NP_055569.1  phosphatidylserine synthase 1 isoform 1

      See identical proteins and their annotated locations for NP_055569.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AP003465, BC004192, BM459031, HY087183
      Consensus CDS
      CCDS6271.1
      UniProtKB/Swiss-Prot
      B4DE85, E5RFC5, P48651, Q9BUQ5
      UniProtKB/TrEMBL
      A8KAH1
      Related
      ENSP00000430548.1, ENST00000517309.6
      Conserved Domains (1) summary
      pfam03034
      Location:96 → 371
      PSS; Phosphatidyl serine synthase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      96261902..96336995
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      97387620..97462689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P48651.1 GenPept UniProtKB/Swiss-Prot:P48651

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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