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Aliases for SMS Gene

Aliases for SMS Gene

  • Spermine Synthase 2 3 5
  • Spermidine Aminopropyltransferase 3 4
  • SPMSY 3 4
  • Snyder-Robinson X-Linked Mental Retardation Syndrome 2
  • EC 2.5.1.22 4
  • MRSR 3
  • SPS 3
  • SRS 3

External Ids for SMS Gene

Previous HGNC Symbols for SMS Gene

  • SRS

Previous GeneCards Identifiers for SMS Gene

  • GC0XP020700
  • GC0XP020548
  • GC0XP021160
  • GC0XP021320
  • GC0XP021718
  • GC0XP021868
  • GC0XP019699

Summaries for SMS Gene

Entrez Gene Summary for SMS Gene

  • This gene encodes a protein belonging to the spermidine/spermin synthase family. Pseudogenes of this gene are located on chromosomes 1, 5, 6 and X. Mutations in this gene are associated with X-linked Snyder-Robinson mental retardation syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

GeneCards Summary for SMS Gene

SMS (Spermine Synthase) is a Protein Coding gene. Diseases associated with SMS include Mental Retardation, X-Linked, Snyder-Robinson Type and Hand Dermatosis. Among its related pathways are Viral mRNA Translation and Urea cycle and metabolism of amino groups. GO annotations related to this gene include spermidine synthase activity and spermine synthase activity.

UniProtKB/Swiss-Prot for SMS Gene

  • Catalyzes the production of spermine from spermidine and decarboxylated S-adenosylmethionine (dcSAM).

Gene Wiki entry for SMS Gene

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

Genomics for SMS Gene

Regulatory Elements for SMS Gene

Enhancers for SMS Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG021971 1.1 Ensembl ENCODE 13.5 +32.7 32729 4.0 CTCF RAD21 TCF12 CTBP1 GATA3 NCOR1 EED ETV6 FOS TRIM24 SMS MBTPS2 YY2 GC0XM021715
GH0XG021958 1 Ensembl ENCODE 8.4 +20.0 19979 3.5 HDGF ZNF146 TAL1 ZMYM3 CEBPG ZNF644 YY1 TCF12 IRF9 ZBTB48 SMS YY2 MBTPS2 GC0XM021715
GH0XG021939 1.3 FANTOM5 ENCODE 6.2 +2.0 1978 5.8 HDGF ATF1 SIN3A DMAP1 YY1 TCF12 ZNF121 GLIS2 FOS KLF13 YY2 SMS GC0XM021715
GH0XG021954 1 Ensembl ENCODE 5.6 +14.7 14667 1.8 CTCF DPF2 CEBPG RAD21 FOXA1 JUND GATA3 CTBP1 ZNF585B ZNF692 SMS YY2 GC0XM021715
GH0XG021989 0.7 FANTOM5 5 +49.0 48968 0.4 MTA2 IKZF1 MLLT1 RELB IKZF2 TBX21 YY2 SMS GC0XM021715 GC0XP022008
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMS on UCSC Golden Path with GeneCards custom track

Promoters for SMS Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000245214 827 2401 HDGF ATF1 SIN3A DMAP1 YY1 ZNF121 GLIS2 FOS KLF13 ZNF263

Genomic Location for SMS Gene

Chromosome:
X
Start:
21,940,573 bp from pter
End:
21,994,837 bp from pter
Size:
54,265 bases
Orientation:
Plus strand

Genomic View for SMS Gene

Genes around SMS on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SMS Gene

Proteins for SMS Gene

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

    Protein Symbol:
    P52788-SPSY_HUMAN
    Recommended name:
    Spermine synthase
    Protein Accession:
    P52788
    Secondary Accessions:
    • A6NHA7
    • A6NI34
    • B2R9M0
    • O00544
    • Q9UQS1

    Protein attributes for SMS Gene

    Size:
    366 amino acids
    Molecular mass:
    41268 Da
    Quaternary structure:
    • Homodimer. Dimerization is mediated through the N-terminal domain and seems to be required for activity as deletion of the N-terminal domain causes complete loss of activity.

    Three dimensional structures from OCA and Proteopedia for SMS Gene

    Alternative splice isoforms for SMS Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMS Gene

Post-translational modifications for SMS Gene

  • Ubiquitination at Lys151
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SMS Gene

Domains & Families for SMS Gene

Protein Domains for SMS Gene

Suggested Antigen Peptide Sequences for SMS Gene

Graphical View of Domain Structure for InterPro Entry

P52788

UniProtKB/Swiss-Prot:

SPSY_HUMAN :
  • Composed of 3 domains: the N-terminal domain has structural similarity to S-adenosylmethionine decarboxylase, the central domain is made up of four beta strands and the C-terminal domain is similar in structure to spermidine synthase. The N- and C-terminal domains are both required for activity.
  • Belongs to the spermidine/spermine synthase family.
Domain:
  • Composed of 3 domains: the N-terminal domain has structural similarity to S-adenosylmethionine decarboxylase, the central domain is made up of four beta strands and the C-terminal domain is similar in structure to spermidine synthase. The N- and C-terminal domains are both required for activity.
Family:
  • Belongs to the spermidine/spermine synthase family.
genes like me logo Genes that share domains with SMS: view

No data available for Gene Families for SMS Gene

Function for SMS Gene

Molecular function for SMS Gene

GENATLAS Biochemistry:
spermine synthase,ubiquitously expressed,polyamine blocking the inwardly rectifying K+ channel present in the inner ear,38kb telomeric to PEX,ubiquitous
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5-thioadenosine + spermine.
UniProtKB/Swiss-Prot Function:
Catalyzes the production of spermine from spermidine and decarboxylated S-adenosylmethionine (dcSAM).

Enzyme Numbers (IUBMB) for SMS Gene

Gene Ontology (GO) - Molecular Function for SMS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity IEA --
GO:0016768 spermine synthase activity TAS,IEA --
genes like me logo Genes that share ontologies with SMS: view
genes like me logo Genes that share phenotypes with SMS: view

Human Phenotype Ontology for SMS Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SMS Gene

MGI Knock Outs for SMS:
  • Sms tm1a(EUCOMM)Wtsi

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMS

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

Localization for SMS 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 SMS gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 3
cytoskeleton 1
mitochondrion 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SMS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with SMS: view

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

Pathways & Interactions for SMS Gene

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

UniProtKB/Swiss-Prot P52788-SPSY_HUMAN

  • Pathway: Amine and polyamine biosynthesis; spermine biosynthesis; spermine from spermidine: step 1/1.

Gene Ontology (GO) - Biological Process for SMS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006555 methionine metabolic process TAS 7546290
GO:0006595 polyamine metabolic process TAS --
GO:0006596 polyamine biosynthetic process IEA --
GO:0006597 spermine biosynthetic process IEA --
GO:0008215 spermine metabolic process IEA --
genes like me logo Genes that share ontologies with SMS: view

No data available for SIGNOR curated interactions for SMS Gene

Drugs & Compounds for SMS Gene

(5) Drugs for SMS Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
spermine Approved Nutra Full agonist, Agonist, Target, ligand 0
putrescine Experimental Pharma Antagonist, Pore Blocker 0
spermidine Experimental Pharma Antagonist, Pore Blocker 0

(7) Additional Compounds for SMS Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
1,3-diaminopropane
  • 1,3-Diamino-N-propane
  • 1,3-Propanediamine
  • 1,3-Propylenediamine
  • 1,3-Trimethylenediamine
  • 3-Aminopropylamine
109-76-2
5'-Methylthioadenosine
  • 1-(6-Amino-9H-purin-9-yl)-1-deoxy-5-S-methyl-5-thio-beta-D-Ribofuranose
  • 1-(6-Amino-9H-purin-9-yl)-1-deoxy-5-S-methyl-5-thio-beta-delta-Ribofuranose
  • 5'-(Methylthio)-5'-deoxyadenosine
  • 5'-(Methylthio)adenosine
  • 5'-Deoxy-5'-(methylthio)adenosine
2457-80-9
N1-acetylspermine
  • N'-Acetylspermine
  • N'-Monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-Acetamide
  • N-Acetylspermine
25593-72-0
Norspermidine
  • -1,3-propanediamine
  • 1,7-Diamino-4-azaheptane
  • 3, 3'-Diaminodipropylamine
  • 3, {3'-Iminobis[propylamine]}
  • 3,3'-Diamino-Dipropylamine
56-18-8
S-Adenosylmethioninamine
  • (5-deoxy-5-adenosyl)(3-aminopropyl) methylsulfonium salt
  • DAdoMet
  • Decarboxylated AdoMet
  • Decarboxylated S-adenosylmethionine
  • Decarboxylated SAM
22365-13-5
genes like me logo Genes that share compounds with SMS: view

Transcripts for SMS Gene

Unigene Clusters for SMS Gene

Spermine synthase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMS

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

No ASD Table

Relevant External Links for SMS Gene

GeneLoc Exon Structure for
SMS
ECgene alternative splicing isoforms for
SMS

Expression for SMS Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMS Gene

This gene is overexpressed in Testis (8.9), Ovary (7.4), and Peripheral blood mononuclear cells (6.2).

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



Protein tissue co-expression partners for SMS Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMS Gene:

SMS

SOURCE GeneReport for Unigene cluster for SMS Gene:

Hs.724874

Evidence on tissue expression from TISSUES for SMS Gene

  • Kidney(4.4)
  • Intestine(4.3)
  • Blood(4.2)
  • Skin(4.1)
  • Nervous system(3.8)
  • Heart(2)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
  • vocal cord
Thorax:
  • breast
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
  • testicle
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SMS: view

Primer Products

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

Orthologs for SMS Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SMS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMS 34
  • 99.57 (n)
dog
(Canis familiaris)
Mammalia SMS 34 35
  • 93.88 (n)
cow
(Bos Taurus)
Mammalia SMS 34 35
  • 93.7 (n)
rat
(Rattus norvegicus)
Mammalia Sms 34
  • 91.8 (n)
mouse
(Mus musculus)
Mammalia Sms 34 16 35
  • 91.26 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 87 (a)
OneToMany
-- 35
  • 73 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SMS 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMS 34 35
  • 81.54 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 90 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia sms 34
  • 75.6 (n)
zebrafish
(Danio rerio)
Actinopterygii sms 34 35
  • 68.8 (n)
LOC80872 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005325 34
  • 53.25 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4300 36 34 35
  • 51.98 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SPE4 35
  • 18 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 51 (a)
OneToMany
-- 35
  • 45 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4694 34
Species where no ortholog for SMS 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)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SMS Gene

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

Paralogs for SMS Gene

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

No data available for Paralogs for SMS Gene

Variants for SMS Gene

Sequence variations from dbSNP and Humsavar for SMS Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs121434610 Pathogenic, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,967,312(+) AGAAC(A/G)GCAGG reference, missense
rs267607076 Pathogenic, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,977,126(+) CCTGG(G/T)TGAAT reference, missense
rs397515549 Pathogenic, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,971,900(+) AGCTT(A/T)GCCAA intron-variant, reference, missense
rs397515550 Pathogenic, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,971,926(+) ACATG(A/G)ATTGG intron-variant, reference, missense
rs397515553 Pathogenic, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,992,634(+) GCTCT(A/C/G)TGAAG reference, missense

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

Variant ID Type Subtype PubMed ID
esv3573638 CNV loss 25503493
esv3573639 CNV loss 25503493
nsv1139393 CNV deletion 24896259
nsv1145287 CNV deletion 24896259
nsv425472 CNV deletion 16902084
nsv6832 CNV deletion 18451855
nsv819785 CNV loss 19587683

Variation tolerance for SMS Gene

Residual Variation Intolerance Score: 13% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.33; 7.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMS Gene

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

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

Disorders for SMS Gene

MalaCards: The human disease database

(4) MalaCards diseases for SMS Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, x-linked, snyder-robinson type
  • mental retardation, x-linked, syndromic, snyder-robinson type
hand dermatosis
  • hand dermatoses
corneal dystrophy, congenital stromal
  • congenital stromal corneal dystrophy
extratemporal epilepsy
- elite association - COSMIC cancer census association via MalaCards
Search SMS in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SPSY_HUMAN
  • X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583]: Characterized by moderate intellectual deficit, hypotonia, an unsteady gait, osteoporosis, kyphoscoliosis and facial asymmetry. Transmission is X-linked recessive. {ECO:0000269 PubMed:14508504, ECO:0000269 PubMed:18550699, ECO:0000269 PubMed:19206178, ECO:0000269 PubMed:22612257, ECO:0000269 PubMed:23696453, ECO:0000269 PubMed:23897707}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SMS

Human Genome Epidemiology (HuGE) Navigator
SMS
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMS
genes like me logo Genes that share disorders with SMS: view

No data available for Genatlas for SMS Gene

Publications for SMS Gene

  1. X-linked spermine synthase gene (SMS) defect: the first polyamine deficiency syndrome. (PMID: 14508504) Cason A.L. … Schwartz C.E. (Eur. J. Hum. Genet. 2003) 2 3 4 25 64
  2. Sequence analysis of 139 kb in Xp22.1 containing spermine synthase and the 5' region of PEX. (PMID: 9299240) Grieff M. … Mazzarella R. (Genomics 1997) 2 3 4 22 64
  3. Molecular cloning of a cDNA encoding human spermine synthase. (PMID: 7546290) Korhonen V.-P. … Jaenne J. (DNA Cell Biol. 1995) 2 3 4 22 64
  4. A missense mutation, p.V132G, in the X-linked spermine synthase gene (SMS) causes Snyder-Robinson syndrome. (PMID: 19206178) Becerra-Solano L.E. … GarcA-a-Ortiz J.E. (Am. J. Med. Genet. A 2009) 3 4 22 64
  5. Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism. (PMID: 18367445) Wu H. … Plotnikov A.N. (J. Biol. Chem. 2008) 3 4 22 64

Products for SMS Gene

Sources for SMS Gene

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