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    SGMS2 sphingomyelin synthase 2 [ Homo sapiens (human) ]

    Gene ID: 166929, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SGMS2provided by HGNC
    Official Full Name
    sphingomyelin synthase 2provided by HGNC
    Primary source
    HGNC:HGNC:28395
    See related
    Ensembl:ENSG00000164023 MIM:611574; AllianceGenome:HGNC:28395
    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
    CDL; SMS2
    Summary
    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]
    Expression
    Broad expression in gall bladder (RPKM 18.4), lung (RPKM 12.8) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SGMS2 in Genome Data Viewer
    Location:
    4q25
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (107824563..107915047)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (111126863..111217333)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (108745719..108836203)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377358 Neighboring gene 3'-phosphoadenosine 5'-phosphosulfate synthase 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:108626049-108626213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21790 Neighboring gene NANOG hESC enhancer GRCh37_chr4:108655227-108655757 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:108748306-108749505 Neighboring gene CYP2U1 and SGMS2 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 733, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:108812473-108813203 Neighboring gene uncharacterized LOC107986298 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:108827506-108828091 Neighboring gene uncharacterized LOC124900751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:108852075-108852582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21792 Neighboring gene uncharacterized LOC107986299 Neighboring gene cytochrome P450 family 2 subfamily U member 1

    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 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. SGMS2 in primary osteoporosis with facial nerve palsy. Pihlström S, et al. Front Endocrinol (Lausanne), 2023. PMID 37886644, Free PMC Article
    2. Identification of SGMS2 as a molecule involved in natural killer cell recruitment and its in-deep analysis in the liver cancer microenvironment: Evidence from large populations cohort. Tang W, et al. J Gene Med, 2024 Jan. PMID 37849429
    3. Clinical and Genetic Characteristics of Calvarial Doughnut Lesions with Bone Fragility in Three Families with a Reccurent SGMS2 Gene Variant. Merkuryeva E, et al. Int J Mol Sci, 2023 Apr 28. PMID 37175737, Free PMC Article
    4. Sphingomyelin synthase SMS2 displays dual activity as ceramide phosphoethanolamine synthase. Ternes P, et al. J Lipid Res, 2009 Nov. PMID 19454763, Free PMC Article
    5. Sphingomyelin synthase 2 is palmitoylated at the COOH-terminal tail, which is involved in its localization in plasma membranes. Tani M, et al. Biochem Biophys Res Commun, 2009 Apr 10. PMID 19233134

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of SGMS2 as a molecule involved in natural killer cell recruitment and its in-deep analysis in the liver cancer microenvironment: Evidence from large populations cohort.
      Title: Identification of SGMS2 as a molecule involved in natural killer cell recruitment and its in-deep analysis in the liver cancer microenvironment: Evidence from large populations cohort.
    2. Sphingomyelin synthase 2 promotes the stemness of breast cancer cells via modulating NF-kappaB signaling pathway.
      Title: Sphingomyelin synthase 2 promotes the stemness of breast cancer cells via modulating NF-κB signaling pathway.
    3. SGMS2 in primary osteoporosis with facial nerve palsy.
      Title: SGMS2 in primary osteoporosis with facial nerve palsy.
    4. Clinical and Genetic Characteristics of Calvarial Doughnut Lesions with Bone Fragility in Three Families with a Reccurent SGMS2 Gene Variant.
      Title: Clinical and Genetic Characteristics of Calvarial Doughnut Lesions with Bone Fragility in Three Families with a Reccurent SGMS2 Gene Variant.
    5. LARP6 suppresses colorectal cancer progression through ZNF267/SGMS2-mediated imbalance of sphingomyelin synthesis.
      Title: LARP6 suppresses colorectal cancer progression through ZNF267/SGMS2-mediated imbalance of sphingomyelin synthesis.
    6. LncRNA THAP9-AS1 accelerates cell growth of esophageal squamous cell carcinoma through sponging miR-335-5p to regulate SGMS2.
      Title: LncRNA THAP9-AS1 accelerates cell growth of esophageal squamous cell carcinoma through sponging miR-335-5p to regulate SGMS2.
    7. Genome-wide association study of serum prostate-specific antigen levels based on 1000 Genomes imputed data in Japanese: the Japan Multi-Institutional Collaborative Cohort Study.
      Title: Genome-wide association study of serum prostate-specific antigen levels based on 1000 Genomes imputed data in Japanese: the Japan Multi-Institutional Collaborative Cohort Study.
    8. Sphingomyelin synthase 2 facilitates M2-like macrophage polarization and tumor progression in a mouse model of triple-negative breast cancer.
      Title: Sphingomyelin synthase 2 facilitates M2-like macrophage polarization and tumor progression in a mouse model of triple-negative breast cancer.
    9. Chlamydia trachomatis-infected human cells convert ceramide to sphingomyelin without sphingomyelin synthases 1 and 2.
      Title: Chlamydia trachomatis-infected human cells convert ceramide to sphingomyelin without sphingomyelin synthases 1 and 2.
    10. SGMS2-dependent signaling was investigated in human monocyte-derived macrophages of nonsmokers and human bronchial epithelial (HBE) cells isolated from healthy nonsmokers and subjects with COPD. Reduced SGMS2 expression was seen in HBE cells isolated from subjects with COPD. SGMS2 overexpression reduced the production of several matrix metalloproteinases in HBE cells and monocyte-derived macrophages.
      Title: Airway Resistance Caused by Sphingomyelin Synthase 2 Insufficiency in Response to Cigarette Smoke.
    Submit: New GeneRIF Correction See all GeneRIFs (30)

    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
    Calvarial doughnut lesions-bone fragility syndrome
    MedGen: C1852022 OMIM: 126550 GeneReviews: Not available
    		Compare labs

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env SMS2 is involved in HIV-1 gp120-induced phosphorylation and activation of PYK2 and polymerization of F-actin PubMed
    env SMS2, but not SMS1, is involved in enhancement of HIV-1 gp120/gp41-mediated membrane fusion through CD4 receptor and CCR5/CXCR4 coreceptors PubMed
    Envelope transmembrane glycoprotein gp41 env SMS2, but not SMS1, is involved in enhancement of HIV-1 gp120/gp41-mediated membrane fusion through CD4 receptor and CCR5/CXCR4 coreceptors PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • MGC26963

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ceramide cholinephosphotransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ceramide cholinephosphotransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ceramide phosphoethanolamine synthase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sphingomyelin synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sphingomyelin synthase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sphingomyelin synthase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in ceramide biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ceramide phosphoethanolamine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of bone mineralization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sphingolipid biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in sphingomyelin biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingomyelin biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    phosphatidylcholine:ceramide cholinephosphotransferase 2
    Names
    SM synthase
    NP_001129729.1
    NP_001129730.1
    NP_001362834.1
    NP_001362835.1
    NP_001362836.1
    NP_001362837.1
    NP_001362839.1
    NP_001362840.1
    NP_689834.1
    XP_011530001.1
    XP_011530003.1
    XP_047305669.1
    XP_047305670.1
    XP_047305671.1
    XP_047305672.1
    XP_047305673.1
    XP_047305674.1
    XP_047305675.1
    XP_054205099.1
    XP_054205100.1
    XP_054205101.1
    XP_054205102.1
    XP_054205103.1
    XP_054205104.1
    XP_054205105.1
    XP_054205106.1
    XP_054205107.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001136257.2 → NP_001129729.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 1

      See identical proteins and their annotated locations for NP_001129729.1

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Consensus CDS
      CCDS3677.1
      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Related
      ENSP00000351981.4, ENST00000359079.8
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    2. NM_001136258.2 → NP_001129730.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 1

      See identical proteins and their annotated locations for NP_001129730.1

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Consensus CDS
      CCDS3677.1
      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Related
      ENSP00000378176.4, ENST00000394684.8
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    3. NM_001375905.1 → NP_001362834.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Consensus CDS
      CCDS3677.1
      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Related
      ENSP00000508566.1, ENST00000690982.1
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    4. NM_001375906.1 → NP_001362835.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Consensus CDS
      CCDS3677.1
      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    5. NM_001375907.1 → NP_001362836.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Consensus CDS
      CCDS3677.1
      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    6. NM_001375908.1 → NP_001362837.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Consensus CDS
      CCDS3677.1
      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    7. NM_001375910.1 → NP_001362839.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Conserved Domains (1) summary
      cl00474
      Location:220 → 242
      PAP2_like; PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid ...

    8. NM_001375911.1 → NP_001362840.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Conserved Domains (1) summary
      pfam14360
      Location:47 → 120
      PAP2_C; PAP2 superfamily C-terminal

    9. NM_152621.6 → NP_689834.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform 1

      See identical proteins and their annotated locations for NP_689834.1

      Status: REVIEWED

      Source sequence(s)
      AC096564
      Consensus CDS
      CCDS3677.1
      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Related
      ENSP00000378178.3, ENST00000394686.3
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      107824563..107915047
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449717.1 → XP_047305673.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    2. XM_011531701.3 → XP_011530003.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      See identical proteins and their annotated locations for XP_011530003.1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    3. XM_047449719.1 → XP_047305675.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X2

    4. XM_047449714.1 → XP_047305670.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    5. XM_047449718.1 → XP_047305674.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X2

    6. XM_047449713.1 → XP_047305669.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    7. XM_047449716.1 → XP_047305672.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    8. XM_047449715.1 → XP_047305671.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    9. XM_011531699.2 → XP_011530001.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      See identical proteins and their annotated locations for XP_011530001.1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
      Conserved Domains (1) summary
      pfam14360
      Location:220 → 293
      PAP2_C; PAP2 superfamily C-terminal

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      111126863..111217333
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349130.1 → XP_054205105.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    2. XM_054349125.1 → XP_054205100.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    3. XM_054349132.1 → XP_054205107.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X2

    4. XM_054349127.1 → XP_054205102.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    5. XM_054349131.1 → XP_054205106.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X2

    6. XM_054349126.1 → XP_054205101.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    7. XM_054349129.1 → XP_054205104.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    8. XM_054349128.1 → XP_054205103.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3

    9. XM_054349124.1 → XP_054205099.1  phosphatidylcholine:ceramide cholinephosphotransferase 2 isoform X1

      UniProtKB/Swiss-Prot
      A8K2S9, B2RA61, Q8NHU3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NHU3.1 GenPept UniProtKB/Swiss-Prot:Q8NHU3

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