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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 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]

GeneCards Summary for SMS Gene

SMS (Spermine Synthase) is a Protein Coding gene. Diseases associated with SMS include Mental Retardation, X-Linked, Syndromic, Snyder-Robinson Type and Syndromic X-Linked Intellectual Disability Snyder Type. Among its related pathways are Urea cycle and metabolism of amino groups and CDK-mediated phosphorylation and removal of Cdc6. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for SMS Gene

Promoters and enhancers for SMS 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
GH0XI021939 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 556.2 +2.0 1977 5.8 ATF1 SIN3A DMAP1 YY1 ZNF121 GLIS2 FOS ATF7 SP3 SP5 SMS YY2 LOC100418871 GC0XM021715
GH0XI021971 Enhancer 0.9 Ensembl ENCODE 13.5 +32.7 32728 4 CTCF SMARCE1 DPF2 ELF1 FOXA1 ZNF217 CTBP1 JUND GATA3 ZNF585B SMS MBTPS2 YY2 GC0XM021715
GH0XI021958 Enhancer 0.8 Ensembl ENCODE 8.4 +20.0 19978 3.5 HDGF ZNF362 TEAD4 HLF TAL1 CBFA2T3 TCF12 ZBTB48 POLR2A SMAD4 SMS YY2 MBTPS2 GC0XM021715
GH0XI021954 Enhancer 0.6 Ensembl ENCODE 5.6 +14.7 14667 1.8 ZNF692 ZNF558 SMS YY2 GC0XM021715
GH0XI021989 Enhancer 0.6 FANTOM5 5 +49.0 48967 0.4 IKZF1 ATF7 MLLT1 IKZF2 ATF2 RUNX3 YY2 SMS GC0XM021715 GC0XP022008
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SMS on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for SMS Gene

Genomic Locations for SMS Gene
chrX:21,940,573-21,994,837
(GRCh38/hg38)
Size:
54,265 bases
Orientation:
Plus strand
chrX:21,958,691-22,025,798
(GRCh37/hg19)

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

No data available for DME Specific Peptides for SMS Gene

Domains & Families for SMS Gene

Gene Families for SMS Gene

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

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

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 IEA,TAS --
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 Model Products

Clone Products

No data available for Phenotypes From GWAS Catalog , Animal Models , 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
See all subcellular structures

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,HDA 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 --
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

(4) 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

(8) 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:

Clone Products

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
Regions:
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

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 33
  • 99.57 (n)
dog
(Canis familiaris)
Mammalia SMS 33 34
  • 93.88 (n)
cow
(Bos Taurus)
Mammalia SMS 33 34
  • 93.7 (n)
rat
(Rattus norvegicus)
Mammalia Sms 33
  • 91.8 (n)
mouse
(Mus musculus)
Mammalia Sms 33 34
  • 91.26 (n)
Sms-ps 16
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 87 (a)
OneToMany
-- 34
  • 73 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SMS 34
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMS 33 34
  • 81.54 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 90 (a)
OneToMany
-- 34
  • 82 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia sms 33
  • 75.6 (n)
zebrafish
(Danio rerio)
Actinopterygii sms 33 34
  • 68.8 (n)
LOC80872 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005325 33
  • 53.25 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4300 35 33 34
  • 51.98 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SPE4 34
  • 18 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 51 (a)
OneToMany
-- 34
  • 45 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4694 33
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 Variation AA Info Type
rs121434610 pathogenic, likely-pathogenic, Snyder Robinson syndrome, Inborn genetic diseases, not provided, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,967,312(+) G/A coding_sequence_variant, missense_variant
rs267607076 pathogenic, Snyder Robinson syndrome, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,977,126(+) T/G coding_sequence_variant, missense_variant
rs397515381 pathogenic, Snyder Robinson syndrome 21,972,576(+) G/A intron_variant
rs397515549 pathogenic, Snyder Robinson syndrome, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,971,900(+) T/A/C coding_sequence_variant, intron_variant, missense_variant, synonymous_variant
rs397515550 pathogenic, Snyder Robinson syndrome, X-linked syndromic mental retardation Snyder-Robinson type (MRXSSR) [MIM:309583] 21,971,926(+) G/A coding_sequence_variant, intron_variant, missense_variant

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

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

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)

Additional Variant Information 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

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

Disorder Aliases PubMed IDs
mental retardation, x-linked, syndromic, snyder-robinson type
  • srs
syndromic x-linked intellectual disability snyder type
  • mental retardation, x-linked, snyder-robinson type
osteoporosis
  • bone mineral density quantitative trait locus; bmnd
- 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.

Additional Disease Information for 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 AL … Schwartz CE (European journal of human genetics : EJHG 2003) 2 3 4 25 58
  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 58
  3. Molecular cloning of a cDNA encoding human spermine synthase. (PMID: 7546290) Korhonen VP … Jänne J (DNA and cell biology 1995) 2 3 4 22 58
  4. A missense mutation, p.V132G, in the X-linked spermine synthase gene (SMS) causes Snyder-Robinson syndrome. (PMID: 19206178) Becerra-Solano LE … García-Ortiz JE (American journal of medical genetics. Part A 2009) 3 4 22 58
  5. Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism. (PMID: 18367445) Wu H … Plotnikov AN (The Journal of biological chemistry 2008) 3 4 22 58

Products for SMS Gene

Sources for SMS Gene

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