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    SMS spermine synthase [ Homo sapiens (human) ]

    Gene ID: 6611, updated on 17-Mar-2024

    Summary

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    Official Symbol
    SMSprovided by HGNC
    Official Full Name
    spermine synthaseprovided by HGNC
    Primary source
    HGNC:HGNC:11123
    See related
    Ensembl:ENSG00000102172 MIM:300105; AllianceGenome:HGNC:11123
    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
    SRS; SpS; MRSR; SPMSY; MRXSSR
    Summary
    This gene encodes a protein belonging to the spermidine/spermin synthase family and catalyzes the production of spermine from spermidine. Pseudogenes of this gene are located on chromosomes 1, 5, 6 and X. Mutations in this gene cause an X-linked intellectual disability called Snyder-Robinson Syndrome (SRS). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
    Expression
    Ubiquitous expression in prostate (RPKM 40.6), placenta (RPKM 32.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMS in Genome Data Viewer
    Location:
    Xp22.11
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (21940709..21994837)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (21524038..21578161)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (21958827..22012955)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29487 Neighboring gene CYTH1 pseudogene 1 Neighboring gene phosphate regulating endopeptidase X-linked Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29488 Neighboring gene PHEX antisense RNA 1 Neighboring gene PTCHD1 antisense RNA (head to head) Neighboring gene Cbl proto-oncogene like 2

    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. Whole-exome sequencing identifies a novel mutation in spermine synthase gene (SMS) associated with Snyder-Robinson Syndrome. Qazi TJ, et al. BMC Med Genet, 2020 Aug 24. PMID 32838743, Free PMC Article
    2. Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase. Peng Y, et al. Int J Mol Sci, 2016 Jan 8. PMID 26761001, Free PMC Article
    3. Snyder-Robinson Syndrome. Adam MP, et al. , 1993. PMID 23805436
    4. A Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome. Zhang Z, et al. Hum Mol Genet, 2013 Sep 15. PMID 23696453, Free PMC Article
    5. Enhancing human spermine synthase activity by engineered mutations. Zhang Z, et al. PLoS Comput Biol, 2013. PMID 23468611, Free PMC Article

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Effects of Spermine Synthase Deficiency in Mesenchymal Stromal Cells Are Rescued by Upstream Inhibition of Ornithine Decarboxylase.
      Title: Effects of Spermine Synthase Deficiency in Mesenchymal Stromal Cells Are Rescued by Upstream Inhibition of Ornithine Decarboxylase.
    2. Whole-exome sequencing identifies a novel mutation in spermine synthase gene (SMS) associated with Snyder-Robinson Syndrome.
      Title: Whole-exome sequencing identifies a novel mutation in spermine synthase gene (SMS) associated with Snyder-Robinson Syndrome.
    3. Spermine synthase and MYC cooperate to maintain colorectal cancer cell survival by repressing Bim expression.
      Title: Spermine synthase and MYC cooperate to maintain colorectal cancer cell survival by repressing Bim expression.
    4. Spermine synthase (SMS) localized together with myosin Va (MyoVa) in cytoplasmic vesicles of breast cancer MCF-7 and neuroblastoma SH-SY5Y cell lines, known to produce exosomes, supporting a role for MyoVa in SMS expression and targeting.
      Title: Myosin Va interacts with the exosomal protein spermine synthase.
    5. Missense mutations causing Snyder-Robinson Syndrome resulting in dysfunctional spermine synthase cause the destabilization of the protein.
      Title: Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase.
    6. Results show that p.Y328C, a missense mutation in SMS is responsible for the patients having a mild form of Snyder-Robinson syndrome.
      Title: A Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome.
    7. Studied human spermine synthase activity by engineered mutations.
      Title: Enhancing human spermine synthase activity by engineered mutations.
    8. This observation is used to demonstrate, computationally and experimentally, that a particular condition, Snyder-Robinson syndrome caused by the G56S spermine synthase mutation, might be ameliorated by small molecule binding.
      Title: A rational free energy-based approach to understanding and targeting disease-causing missense mutations.
    9. spermine synthase activity and the resulting elevation of the spermine:spermidine ratio does not alter susceptibility to tumor development initiated by c-Ha-Ras mutation or Apc loss
      Title: Spermine synthase overexpression in vivo does not increase susceptibility to DMBA/TPA skin carcinogenesis or Min-Apc intestinal tumorigenesis.
    10. the mutability of spermine synthase
      Title: In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    Syndromic X-linked intellectual disability Snyder type
    MedGen: C0796160 OMIM: 309583 GeneReviews: Snyder-Robinson Syndrome
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2012-08-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2012-08-23)

    ClinGen Genome Curation PagePubMed

    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables spermine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables spermine synthase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in methionine metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in polyamine metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in spermine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 

    General protein information

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    Preferred Names
    spermine synthase
    Names
    spermidine aminopropyltransferase
    NP_001245352.1
    NP_004586.2
    XP_005274639.1
    XP_011543870.1
    XP_054183596.1

    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_009228.1 RefSeqGene

      Range
      4986..59114
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001258423.2 → NP_001245352.1  spermine synthase isoform 2

      See identical proteins and their annotated locations for NP_001245352.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      U53331, U73023
      Consensus CDS
      CCDS59161.1
      UniProtKB/TrEMBL
      B4DE40
      Related
      ENSP00000368714.1, ENST00000379404.5
      Conserved Domains (1) summary
      pfam01564
      Location:67 → 313
      Spermine_synth; Spermine/spermidine synthase

    2. NM_004595.5 → NP_004586.2  spermine synthase isoform 1

      See identical proteins and their annotated locations for NP_004586.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AD001528, BC009898, U73023
      Consensus CDS
      CCDS14203.1
      UniProtKB/Swiss-Prot
      A6NHA7, A6NI34, B2R9M0, O00544, P52788, Q9UQS1
      Related
      ENSP00000385746.2, ENST00000404933.7
      Conserved Domains (3) summary
      pfam01564
      Location:175 → 365
      Spermine_synth; Spermine/spermidine synthase domain
      pfam17284
      Location:123 → 172
      Spermine_synt_N; Spermidine synthase tetramerisation domain
      pfam17950
      Location:21 → 117
      SpmSyn_N; S-adenosylmethionine decarboxylase N -terminal

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      21940709..21994837
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545568.3 → XP_011543870.1  spermine synthase isoform X1

      See identical proteins and their annotated locations for XP_011543870.1

      Conserved Domains (3) summary
      pfam01564
      Location:141 → 331
      Spermine_synth; Spermine/spermidine synthase domain
      pfam17284
      Location:89 → 138
      Spermine_synt_N; Spermidine synthase tetramerisation domain
      pfam17950
      Location:1 → 83
      SpmSyn_N; S-adenosylmethionine decarboxylase N -terminal

    2. XM_005274582.3 → XP_005274639.1  spermine synthase isoform X1

      See identical proteins and their annotated locations for XP_005274639.1

      Conserved Domains (3) summary
      pfam01564
      Location:141 → 331
      Spermine_synth; Spermine/spermidine synthase domain
      pfam17284
      Location:89 → 138
      Spermine_synt_N; Spermidine synthase tetramerisation domain
      pfam17950
      Location:1 → 83
      SpmSyn_N; S-adenosylmethionine decarboxylase N -terminal

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      21524038..21578161
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327621.1 → XP_054183596.1  spermine synthase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P52788.2 GenPept UniProtKB/Swiss-Prot:P52788

    Gene LinkOut

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

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