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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
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Genomic context

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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
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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

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