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Aliases for SGMS2 Gene

Aliases for SGMS2 Gene

  • Sphingomyelin Synthase 2 2 3 4 5
  • EC 2.7.8.27 4 58
  • SMS2 3 4
  • Phosphatidylcholine:Ceramide Cholinephosphotransferase 2 3
  • SM Synthase 3

External Ids for SGMS2 Gene

Previous GeneCards Identifiers for SGMS2 Gene

  • GC04P108966
  • GC04P108745
  • GC04P104477

Summaries for SGMS2 Gene

Entrez Gene Summary for SGMS2 Gene

  • Sphingomyelin, a major component of cell and Golgi membranes, is made by the transfer of phosphocholine from phosphatidylcholine onto ceramide, with diacylglycerol as a side product. The protein encoded by this gene is an enzyme that catalyzes this reaction primarily at the cell membrane. The synthesis is reversible, and this enzyme can catalyze the reaction in either direction. The encoded protein is required for cell growth. Three transcript variants encoding the same protein have been found for this gene. There is evidence for more variants, but the full-length nature of their transcripts has not been determined.[provided by RefSeq, Oct 2008]

GeneCards Summary for SGMS2 Gene

SGMS2 (Sphingomyelin Synthase 2) is a Protein Coding gene. Among its related pathways are Metabolism and Sphingolipid metabolism. GO annotations related to this gene include kinase activity and ceramide cholinephosphotransferase activity. An important paralog of this gene is SGMS1.

UniProtKB/Swiss-Prot for SGMS2 Gene

  • Sphingomyelin synthases synthesize the sphingolipid, sphingomyelin, through transfer of the phosphatidyl head group, phosphatidylcholine, on to the primary hydroxyl of ceramide. The reaction is bidirectional depending on the respective levels of the sphingolipid and ceramide. Plasma membrane SMS2 can also convert phosphatidylethanolamine (PE) to ceramide phosphatidylethanolamine (CPE). Major form in liver. Required for cell growth in certain cell types. Regulator of cell surface levels of ceramide, an important mediator of signal transduction and apoptosis. Regulation of sphingomyelin (SM) levels at the cell surface affects insulin sensitivity.

Additional gene information for SGMS2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SGMS2 Gene

Genomics for SGMS2 Gene

Regulatory Elements for SGMS2 Gene

Enhancers for SGMS2 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
GH04H107895 1.1 Ensembl ENCODE 21.6 +72.4 72377 2 FOXA2 KLF1 JUN FEZF1 BATF GATA3 POLR2A RCOR1 FOSL2 FOS SGMS2 RNU6-733P CYP2U1
GH04H107861 1.6 FANTOM5 Ensembl ENCODE dbSUPER 7 +38.7 38705 3 NFIB JUN MAX BMI1 RAD21 ZFHX2 POLR2A FOS ZNF600 EGR2 SGMS2 HADH RNU6-733P
GH04H107837 1.2 FANTOM5 Ensembl ENCODE dbSUPER 8.3 +14.1 14121 2 FEZF1 SGMS2 RNU6-733P
GH04H107801 0.5 ENCODE 19.1 -22.4 -22373 1 OSR2 FEZF1 ZBTB20 SGMS2 PAPSS1 GC04P107803 GC04P107734
GH04H107799 0.5 Ensembl ENCODE 18.5 -24.0 -24011 1 SGMS2 PAPSS1 LOC101929595 GC04P107803 GC04P107734
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SGMS2 on UCSC Golden Path with GeneCards custom track

Promoters for SGMS2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000171662 1265 2801 FOXA2 SIN3A FEZF1 YY1 ZNF121 GLIS2 FOS SP3 SP5 REST

Genomic Location for SGMS2 Gene

Chromosome:
4
Start:
107,824,335 bp from pter
End:
107,915,047 bp from pter
Size:
90,713 bases
Orientation:
Plus strand

Genomic View for SGMS2 Gene

Genes around SGMS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SGMS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SGMS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SGMS2 Gene

Proteins for SGMS2 Gene

  • Protein details for SGMS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NHU3-SMS2_HUMAN
    Recommended name:
    Phosphatidylcholine:ceramide cholinephosphotransferase 2
    Protein Accession:
    Q8NHU3
    Secondary Accessions:
    • A8K2S9
    • B2RA61

    Protein attributes for SGMS2 Gene

    Size:
    365 amino acids
    Molecular mass:
    42280 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Overexpression of the human protein in mouse causes increased non-HDL-sphingomyelin and non-HDL cholesterol levels, decreased HDL-sphingomyelin and HDL-cholesterol levels and increases lipoprotein atherogenic potential.

neXtProt entry for SGMS2 Gene

Selected DME Specific Peptides for SGMS2 Gene

Q8NHU3:
  • LTLTYLFIKEYSPR
  • TLYLYRCITMYVTTLPVPGMHF
  • VVHERVPPKE
  • AYYITTRLFWWYH
  • GGGLSITGSH

Post-translational modifications for SGMS2 Gene

  • Palmitoylated on Cys-331, Cys-332, Cys-343 and Cys-348; which plays an important role in plasma membrane localization.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for SGMS2 Gene

Gene Families for SGMS2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SGMS2 Gene

Suggested Antigen Peptide Sequences for SGMS2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8NHU3

UniProtKB/Swiss-Prot:

SMS2_HUMAN :
  • Belongs to the sphingomyelin synthase family.
Family:
  • Belongs to the sphingomyelin synthase family.
genes like me logo Genes that share domains with SGMS2: view

Function for SGMS2 Gene

Molecular function for SGMS2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
A ceramide + a phosphatidylcholine = a sphingomyelin + a 1,2-diacyl-sn-glycerol.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by bacterial PC-phospholipase C inhibitor D609.
UniProtKB/Swiss-Prot Function:
Sphingomyelin synthases synthesize the sphingolipid, sphingomyelin, through transfer of the phosphatidyl head group, phosphatidylcholine, on to the primary hydroxyl of ceramide. The reaction is bidirectional depending on the respective levels of the sphingolipid and ceramide. Plasma membrane SMS2 can also convert phosphatidylethanolamine (PE) to ceramide phosphatidylethanolamine (CPE). Major form in liver. Required for cell growth in certain cell types. Regulator of cell surface levels of ceramide, an important mediator of signal transduction and apoptosis. Regulation of sphingomyelin (SM) levels at the cell surface affects insulin sensitivity.

Enzyme Numbers (IUBMB) for SGMS2 Gene

Phenotypes From GWAS Catalog for SGMS2 Gene

Gene Ontology (GO) - Molecular Function for SGMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002950 ceramide phosphoethanolamine synthase activity IEA --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
GO:0033188 sphingomyelin synthase activity TAS --
GO:0047493 ceramide cholinephosphotransferase activity IDA 14685263
genes like me logo Genes that share ontologies with SGMS2: view
genes like me logo Genes that share phenotypes with SGMS2: view

Animal Models for SGMS2 Gene

MGI Knock Outs for SGMS2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SGMS2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SGMS2 Gene

Localization for SGMS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SGMS2 Gene

Cell membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein. Note=Predominantly plasma membrane, some in Golgi apparatus. Some localization in the perinuclear region where it colocalizes with a sialyltransferase.

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 SGMS2 gene
Compartment Confidence
plasma membrane 5
golgi apparatus 5
endoplasmic reticulum 3
peroxisome 2
endosome 1

Gene Ontology (GO) - Cellular Components for SGMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IDA 14685263
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 14685263
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SGMS2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SGMS2 Gene

Pathways & Interactions for SGMS2 Gene

genes like me logo Genes that share pathways with SGMS2: view

Gene Ontology (GO) - Biological Process for SGMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0006686 sphingomyelin biosynthetic process IDA 14685263
GO:0016310 phosphorylation IEA --
GO:0030148 sphingolipid biosynthetic process TAS --
genes like me logo Genes that share ontologies with SGMS2: view

No data available for SIGNOR curated interactions for SGMS2 Gene

Drugs & Compounds for SGMS2 Gene

(2) Drugs for SGMS2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cytidine monophosphate Experimental Pharma 0
Citicoline Investigational Pharma 0

(49) Additional Compounds for SGMS2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Cer(d18:0/12:0)
Cer(d18:0/14:0)
Cer(d18:0/16:0)
Cer(d18:0/18:0)
Cer(d18:0/18:1(11Z))
genes like me logo Genes that share compounds with SGMS2: view

Transcripts for SGMS2 Gene

Unigene Clusters for SGMS2 Gene

Sphingomyelin synthase 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SGMS2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for SGMS2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: - - - - -
SP2: - - -
SP3: - - - - - -
SP4: - - - - - -
SP5: - - - - - - -
SP6: - -
SP7:
SP8:

Relevant External Links for SGMS2 Gene

GeneLoc Exon Structure for
SGMS2
ECgene alternative splicing isoforms for
SGMS2

Expression for SGMS2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SGMS2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SGMS2 Gene:

SGMS2

SOURCE GeneReport for Unigene cluster for SGMS2 Gene:

Hs.595423

mRNA Expression by UniProt/SwissProt for SGMS2 Gene:

Q8NHU3-SMS2_HUMAN
Tissue specificity: Brain, heart, kidney, liver, muscle and stomach. Also expressed in a number of cell lines such as carcinoma HeLa cells, hepatoma Hep-G2 cells, and colon carcinoma Caco-2 cells.
genes like me logo Genes that share expression patterns with SGMS2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SGMS2 Gene

Orthologs for SGMS2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SGMS2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SGMS2 33 34
  • 99.91 (n)
dog
(Canis familiaris)
Mammalia SGMS2 33 34
  • 92.24 (n)
oppossum
(Monodelphis domestica)
Mammalia SGMS2 34
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SGMS2 34
  • 91 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SGMS2 33 34
  • 90.05 (n)
rat
(Rattus norvegicus)
Mammalia Sgms2 33
  • 87.12 (n)
mouse
(Mus musculus)
Mammalia Sgms2 33 16 34
  • 85.66 (n)
chicken
(Gallus gallus)
Aves SGMS2 33 34
  • 80.55 (n)
lizard
(Anolis carolinensis)
Reptilia SGMS2 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sgms2 33
  • 73.79 (n)
zebrafish
(Danio rerio)
Actinopterygii sgms2 33 34
  • 62.93 (n)
SGMS2 (1 of 2) 34
  • 54 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sms-2 34
  • 27 (a)
ManyToMany
sms-1 34
  • 24 (a)
ManyToMany
sms-3 34
  • 20 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10588 34
  • 42 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5178 33
Species where no ortholog for SGMS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)

Evolution for SGMS2 Gene

ENSEMBL:
Gene Tree for SGMS2 (if available)
TreeFam:
Gene Tree for SGMS2 (if available)

Paralogs for SGMS2 Gene

Paralogs for SGMS2 Gene

(3) SIMAP similar genes for SGMS2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SGMS2: view

Variants for SGMS2 Gene

Sequence variations from dbSNP and Humsavar for SGMS2 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs10000006 -- 107,905,227(+) aggca(C/T)gtttt intron-variant
rs1000039297 -- 107,882,134(+) AGTGG(A/G)ATAGC intron-variant
rs1000080090 -- 107,868,974(+) ACACC(A/G)TTTTT intron-variant
rs10000815 -- 107,874,412(+) ATGCG(C/T)CATTC intron-variant
rs1000093745 -- 107,898,454(+) GCCTG(-/T)TTTTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SGMS2 Gene

Variant ID Type Subtype PubMed ID
esv21916 CNV loss 19812545
esv2677080 CNV deletion 23128226
nsv4457 CNV insertion 18451855
nsv461611 CNV loss 19166990
nsv473076 CNV novel sequence insertion 20440878
nsv595120 CNV loss 21841781
nsv830031 CNV gain 17160897

Variation tolerance for SGMS2 Gene

Residual Variation Intolerance Score: 28.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.94; 19.38% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SGMS2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SGMS2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SGMS2 Gene

Disorders for SGMS2 Gene

Relevant External Links for SGMS2

Genetic Association Database (GAD)
SGMS2
Human Genome Epidemiology (HuGE) Navigator
SGMS2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SGMS2

No disorders were found for SGMS2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SGMS2 Gene

Publications for SGMS2 Gene

  1. Sphingomyelin synthase 2 is palmitoylated at the COOH-terminal tail, which is involved in its localization in plasma membranes. (PMID: 19233134) Tani M … Kuge O (Biochemical and biophysical research communications 2009) 3 4 22 60
  2. Identification of a family of animal sphingomyelin synthases. (PMID: 14685263) Huitema K … Holthuis JC (The EMBO journal 2004) 2 3 4 60
  3. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PMID: 20332099) Kalsi G … Riley BP (Human molecular genetics 2010) 3 45 60
  4. The domain responsible for sphingomyelin synthase (SMS) activity. (PMID: 18694848) Yeang C … Jiang XC (Biochimica et biophysica acta 2008) 3 4 60
  5. Both sphingomyelin synthases SMS1 and SMS2 are required for sphingomyelin homeostasis and growth in human HeLa cells. (PMID: 17449912) Tafesse FG … Holthuis JC (The Journal of biological chemistry 2007) 3 4 60

Products for SGMS2 Gene

Sources for SGMS2 Gene

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