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... See more...

Aliases for SGMS2 Gene

Aliases for SGMS2 Gene

  • Sphingomyelin Synthase 2 2 3 4 5
  • SMS2 2 3 4
  • Phosphatidylcholine:Ceramide Cholinephosphotransferase 2 3 4
  • EC 2.7.8.27 4 50
  • SM Synthase 3
  • MGC26963 2
  • SGMS2 5
  • CDL 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. Diseases associated with SGMS2 include Calvarial Doughnut Lesions With Bone Fragility and Atrial Septal Defect 4. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include kinase activity and ceramide cholinephosphotransferase activity. An important paralog of this gene is SGMS1.

UniProtKB/Swiss-Prot Summary for SGMS2 Gene

  • Sphingomyelin synthase that primarily contributes to sphingomyelin synthesis and homeostasis at the plasma membrane. Catalyzes the reversible transfer of phosphocholine moiety in sphingomyelin biosynthesis: in the forward reaction transfers phosphocholine head group of phosphatidylcholine (PC) on to ceramide (CER) to form ceramide phosphocholine (sphingomyelin, SM) and diacylglycerol (DAG) as by-product, and in the reverse reaction transfers phosphocholine from SM to DAG to form PC and CER. The direction of the reaction appears to depend on the levels of CER and DAG in the plasma membrane (PubMed:14685263, PubMed:17449912, PubMed:17982138, PubMed:18370930). Does not use free phosphorylcholine or CDP-choline as donors (PubMed:14685263). Can also transfer phosphoethanolamine head group of phosphatidylethanolamine (PE) on to ceramide (CER) to form ceramide phosphoethanolamine (CPE) (PubMed:19454763). Regulates receptor-mediated signal transduction via mitogenic DAG and proapoptotic CER, as well as via SM, a structural component of membrane rafts that serve as platforms for signal transduction and protein sorting (PubMed:17449912, PubMed:17982138). To a lesser extent, plays a role in secretory transport via regulation of DAG pool at the Golgi apparatus and its downstream effects on PRKD1 (PubMed:18370930, PubMed:21980337). Required for normal bone matrix mineralization (PubMed:30779713).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SGMS2 Gene

Genomics for SGMS2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SGMS2 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
GH04J107823 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 +2.4 2438 5 ZNF600 JUND ATF2 ATF3 YY1 CEBPB FEZF1 ZNF639 ZNF341 MAX HSALNG0036263 SGMS2 lnc-PAPSS1-2 lnc-SGMS2-3 PAPSS1 RF00026-785 RNU6-733P CYP2U1
GH04J107893 Promoter/Enhancer 0.5 EPDnew Ensembl 250.2 +69.9 69855 1 SGMS2 ENSG00000249604 lnc-CYP2U1-1 RF00026-785 RNU6-733P CYP2U1 lnc-SGMS2-3 CYP2U1-AS1
GH04J107895 Enhancer 0.9 Ensembl ENCODE 21.7 +73.2 73156 3.2 JUND CEBPB FEZF1 EP300 FOXA2 STAT3 PRDM6 BATF FOXA1 DPF2 SGMS2 lnc-CYP2U1-1 RF00026-785 RNU6-733P CYP2U1 lnc-SGMS2-3 CYP2U1-AS1
GH04J107861 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 7.1 +39.5 39544 3.6 ZNF600 NFIC ELF1 STAT3 JUND HNF4A ZNF530 BMI1 RAD21 RFX1 SGMS2 HADH RNU6-733P RF00026-785 lnc-PAPSS1-2 lnc-SGMS2-3 CYP2U1 CYP2U1-AS1
GH04J107801 Enhancer 0.4 ENCODE 19.1 -21.7 -21682 1.1 FEZF1 OSR2 ZBTB20 SGMS2 PAPSS1 piR-35674-396 HSALNG0036259
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SGMS2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SGMS2

Top Transcription factor binding sites by QIAGEN in the SGMS2 gene promoter:
  • C/EBPbeta
  • Cart-1
  • COUP
  • COUP-TF
  • COUP-TF1
  • GATA-1
  • HNF-4alpha1
  • HNF-4alpha2
  • LyF-1
  • TBP

Genomic Locations for SGMS2 Gene

Latest Assembly
chr4:107,823,645-107,915,047
(GRCh38/hg38)
Size:
91,403 bases
Orientation:
Plus strand

Previous Assembly
chr4:108,745,719-108,836,203
(GRCh37/hg19 by Entrez Gene)
Size:
90,485 bases
Orientation:
Plus strand

chr4:108,745,719-108,836,203
(GRCh37/hg19 by Ensembl)
Size:
90,485 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 the atherogenic potential of non-HDL lipoprotein particles.

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:
  • Sphingomyelin synthase 2 (SMS2_HUMAN)

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 Function:
Sphingomyelin synthase that primarily contributes to sphingomyelin synthesis and homeostasis at the plasma membrane. Catalyzes the reversible transfer of phosphocholine moiety in sphingomyelin biosynthesis: in the forward reaction transfers phosphocholine head group of phosphatidylcholine (PC) on to ceramide (CER) to form ceramide phosphocholine (sphingomyelin, SM) and diacylglycerol (DAG) as by-product, and in the reverse reaction transfers phosphocholine from SM to DAG to form PC and CER. The direction of the reaction appears to depend on the levels of CER and DAG in the plasma membrane (PubMed:14685263, PubMed:17449912, PubMed:17982138, PubMed:18370930). Does not use free phosphorylcholine or CDP-choline as donors (PubMed:14685263). Can also transfer phosphoethanolamine head group of phosphatidylethanolamine (PE) on to ceramide (CER) to form ceramide phosphoethanolamine (CPE) (PubMed:19454763). Regulates receptor-mediated signal transduction via mitogenic DAG and proapoptotic CER, as well as via SM, a structural component of membrane rafts that serve as platforms for signal transduction and protein sorting (PubMed:17449912, PubMed:17982138). To a lesser extent, plays a role in secretory transport via regulation of DAG pool at the Golgi apparatus and its downstream effects on PRKD1 (PubMed:18370930, PubMed:21980337). Required for normal bone matrix mineralization (PubMed:30779713).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phosphocholine + an N-acylsphing-4-enine = a 1,2-diacyl-sn-glycerol + a sphingomyelin; Xref=Rhea:RHEA:18765, ChEBI:CHEBI:17636, ChEBI:CHEBI:17815, ChEBI:CHEBI:52639, ChEBI:CHEBI:57643; EC=2.7.8.27; Evidence={ECO:0000269|PubMed:14685263, ECO:0000269|PubMed:17449912, ECO:0000269|PubMed:17982138, ECO:0000269|PubMed:18370930};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=1,2-dihexadecanoyl-sn-glycero-3-phosphocholine + an N-acylsphing-4-enine = 1,2-dihexadecanoyl-sn-glycerol + a sphingomyelin; Xref=Rhea:RHEA:43324, ChEBI:CHEBI:17636, ChEBI:CHEBI:52639, ChEBI:CHEBI:72999, ChEBI:CHEBI:82929; Evidence={ECO:0000269|PubMed:14685263};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=1-(9Z-octadecenoyl)-2-acyl-sn-3-glycerol + a sphingomyelin = a 1-(9Z-octadecenoyl)-2-acyl-sn-glycero-3-phosphocholine + an N-acylsphing-4-enine; Xref=Rhea:RHEA:43320, ChEBI:CHEBI:17636, ChEBI:CHEBI:52639, ChEBI:CHEBI:78421, ChEBI:CHEBI:82983; Evidence={ECO:0000269|PubMed:14685263};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phosphocholine + N-hexadecanoylsphinganine = a 1,2-diacyl-sn-glycerol + N-hexadecanoyl-sphinganine-1-phosphocholine; Xref=Rhea:RHEA:41796, ChEBI:CHEBI:17815, ChEBI:CHEBI:57643, ChEBI:CHEBI:67042, ChEBI:CHEBI:78647; Evidence={ECO:0000269|PubMed:19454763};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phosphocholine + N-hexadecanoyl-(4R)-hydroxysphinganine = a 1,2-diacyl-sn-glycerol + N-hexadecanoyl-(4R)-hydroxysphinganine-phosphocholine; Xref=Rhea:RHEA:42140, ChEBI:CHEBI:17815, ChEBI:CHEBI:57643, ChEBI:CHEBI:65107, ChEBI:CHEBI:78650; Evidence={ECO:0000269|PubMed:19454763};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + N-hexadecanoylsphinganine = a 1,2-diacyl-sn-glycerol + N-hexadecanoyl-sphinganine-1-phosphoethanolamine; Xref=Rhea:RHEA:42128, ChEBI:CHEBI:17815, ChEBI:CHEBI:64612, ChEBI:CHEBI:67042, ChEBI:CHEBI:78654; Evidence={ECO:0000269|PubMed:19454763};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + N-hexadecanoyl-(4R)-hydroxysphinganine = a 1,2-diacyl-sn-glycerol + N-hexadecanoyl-(4R)-hydroxysphinganine-1-phosphoethanolamine; Xref=Rhea:RHEA:42144, ChEBI:CHEBI:17815, ChEBI:CHEBI:64612, ChEBI:CHEBI:65107, ChEBI:CHEBI:78656; Evidence={ECO:0000269|PubMed:19454763};.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by bacterial PC-phospholipase C inhibitor D609.

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:0005515 protein binding IPI 32296183
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
GO:0033188 sphingomyelin synthase activity TAS --
genes like me logo Genes that share ontologies with SGMS2: view
genes like me logo Genes that share phenotypes with SGMS2: view

Human Phenotype Ontology for SGMS2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SGMS2 Gene

MGI Knock Outs for SGMS2:

miRNA for SGMS2 Gene

miRTarBase miRNAs that target SGMS2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SGMS2

No data available for 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=Primarily localized at the plasma membrane with a small fraction at the Golgi apparatus. {ECO:0000269 PubMed:14685263}.

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
mitochondrion 2
peroxisome 2
extracellular 1
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SGMS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005794 Golgi apparatus IDA 14685263
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA,IDA 14685263
GO:0016020 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

UniProtKB/Swiss-Prot Q8NHU3-SMS2_HUMAN

  • Pathway: Sphingolipid metabolism.

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 IBA,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

(4) Drugs for SGMS2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Citicoline Approved, Experimental Pharma 0
Ceramide NG Experimental Pharma 0
Cytidine monophosphate Experimental Pharma 0
L-Dilinoleoyllecithin Experimental Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Beta-Cortolone
  • 1-Palmityl-2-palmitoleoyl-sn-glycero-3-phosphocholine
  • Gpcho(16:0/16:1)
  • Gpcho(16:0/16:1n7)
  • Gpcho(16:0/16:1W7)
  • Gpcho(32:1)
CE(22:0)
  • 1-Tetradecanoyl-2-octadecanoyl-sn-glycero-3-phosphocholine
  • GPCho(14:0/18:0)
  • Phosphatidylcholine(14:0/18:0)
  • 1-Myristoyl-2-stearoylphosphatidylcholine
  • 1m-2S-PC
61510-09-6
Cer(d18:0/12:0)
  • C12:0 DHCer
  • N-(Dodecanoyl)-sphinganine
  • N-Dodecanoyldihydrosphingosine
  • N-Lauroyldihydrosphingosine
  • N-Lauroylsphinganine
Cer(d18:0/14:0)
  • C14DH Cer
  • DHC-a 18:0/14:0
  • N-(Myristoyl)-dihydroceramide
  • N-(Tetradecanoyl)-dihydroceramide
  • N-(Tetradecanoyl)-sphinganine
67030-48-2
Cer(d18:0/16:0)
  • C16DH Cer
  • DHC-a 18:0/16:0
  • N-(Hexadecanoyl)-dihydroceramide
  • N-(Hexadecanoyl)-sphinganine
  • N-(Palmitoyl)-dihydroceramide
5966-29-0
genes like me logo Genes that share compounds with SGMS2: view

Transcripts for SGMS2 Gene

mRNA/cDNA for SGMS2 Gene

9 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SGMS2

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

Expression for SGMS2 Gene

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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.

Evidence on tissue expression from TISSUES for SGMS2 Gene

  • Nervous system(2.1)
  • Liver(2.1)
genes like me logo Genes that share expression patterns with SGMS2: view

Primer products for research

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 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 29 30
  • 99.91 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SGMS2 29 30
  • 92.24 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SGMS2 30
  • 91 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SGMS2 30
  • 91 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SGMS2 29 30
  • 90.05 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sgms2 29
  • 87.12 (n)
Mouse
(Mus musculus)
Mammalia Sgms2 29 16 30
  • 85.66 (n)
OneToOne
Chicken
(Gallus gallus)
Aves SGMS2 29 30
  • 80.55 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SGMS2 30
  • 87 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sgms2 29
  • 73.79 (n)
Zebrafish
(Danio rerio)
Actinopterygii sgms2 29 30
  • 62.93 (n)
OneToMany
SGMS2 (1 of 2) 30
  • 54 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea sms-2 30
  • 27 (a)
ManyToMany
sms-1 30
  • 24 (a)
ManyToMany
sms-3 30
  • 20 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10588 30
  • 42 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.5178 29
Species where no ortholog for SGMS2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
Aminode:
Evolutionary constrained regions (ECRs) for SGMS2: view image
Alliance of Genome Resources:
Additional Orthologs for SGMS2

Paralogs for SGMS2 Gene

Paralogs for SGMS2 Gene

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

  • SMS2_HUMAN
  • E5RGG5_HUMAN
  • E5RJ63_HUMAN
  • E5RJU3_HUMAN
genes like me logo Genes that share paralogs with SGMS2: view

Variants for SGMS2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SGMS2 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs1560667389 Likely Pathogenic: Doughnut lesions of skull, familial; Inborn genetic diseases 107,895,701(+) C/T
NM_152621.5(SGMS2):c.148C>T (p.Arg50Ter)
NONSENSE
rs1560667512 Pathogenic: CALVARIAL DOUGHNUT LESIONS WITH BONE FRAGILITY AND SPONDYLOMETAPHYSEAL DYSPLASIA 107,895,738(+) T/G
NM_152621.5(SGMS2):c.185T>G (p.Ile62Ser)
MISSENSE
rs1560667521 Pathogenic: CALVARIAL DOUGHNUT LESIONS WITH BONE FRAGILITY AND SPONDYLOMETAPHYSEAL DYSPLASIA 107,895,744(+) T/G
NM_152621.5(SGMS2):c.191T>G (p.Met64Arg)
MISSENSE
rs9998850 Benign: not provided 107,903,355(+) G/A
NM_001136257.2(SGMS2):c.696G>A (p.Thr232=)
SYNONYMOUS
VAR_082675 Calvarial doughnut lesions with bone fragility and spondylometaphyseal dysplasia (CDLSMD) [MIM:126550] p.Ile62Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SGMS2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for SGMS2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SGMS2
Leiden Open Variation Database (LOVD)
SGMS2

SNP Genotyping and Copy Number Assays for research

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

Disorders for SGMS2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SGMS2 Gene - From: OMI, CVR, GTR, COP, and GCD

Disorder Aliases PubMed IDs
calvarial doughnut lesions with bone fragility
  • cdl
atrial septal defect 4
  • asd4
osteoporosis
  • bone mineral density quantitative trait locus; bmnd
- elite association - COSMIC cancer census association via MalaCards
Search SGMS2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SMS2_HUMAN
  • Calvarial doughnut lesions with bone fragility (CDL) [MIM:126550]: A rare autosomal dominant bone disease characterized by low bone density, distinctive X-ray translucencies of the skull, multiple fractures, elevated serum alkaline phosphatase, and dental caries. Patients present with childhood onset of primary osteoporosis and typical sclerotic doughnut-shaped lesions in the cranial bones. {ECO:0000269 PubMed:30779713}. Note=The disease may be caused by variants affecting the gene represented in this entry.
  • Calvarial doughnut lesions with bone fragility and spondylometaphyseal dysplasia (CDLSMD) [MIM:126550]: A severe form of calvarial doughnut lesions with bone fragility, a rare autosomal dominant disease characterized by low bone density, distinctive X-ray translucencies of the skull, multiple fractures, elevated serum alkaline phosphatase, and dental caries. CDLSMD patients show neonatal onset of fractures, severe short stature, marked cranial sclerosis, and spondylometaphyseal dysplasia. {ECO:0000269 PubMed:30779713}. Note=The disease may be caused by variants affecting the gene represented in this entry.

Additional Disease Information for SGMS2

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SGMS2: view

No data available for Genatlas for SGMS2 Gene

Publications for SGMS2 Gene

  1. Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2. (PMID: 30779713) Pekkinen M … Mäkitie O (JCI insight 2019) 3 4 72
  2. 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
  3. Identification of a family of animal sphingomyelin synthases. (PMID: 14685263) Huitema K … Holthuis JC (The EMBO journal 2004) 2 3 4
  4. Sphingomyelin synthases regulate protein trafficking and secretion. (PMID: 21980337) Subathra M … Luberto C (PloS one 2011) 3 4
  5. 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 40

Products for SGMS2 Gene

Sources for SGMS2 Gene