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    ST3GAL5 ST3 beta-galactoside alpha-2,3-sialyltransferase 5 [ Homo sapiens (human) ]

    Gene ID: 8869, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ST3GAL5provided by HGNC
    Official Full Name
    ST3 beta-galactoside alpha-2,3-sialyltransferase 5provided by HGNC
    Primary source
    HGNC:HGNC:10872
    See related
    Ensembl:ENSG00000115525 MIM:604402; AllianceGenome:HGNC:10872
    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
    SATI; SIAT9; SPDRS; ST3GalV; SIATGM3S; ST3Gal V
    Summary
    Ganglioside GM3 is known to participate in the induction of cell differentiation, modulation of cell proliferation, maintenance of fibroblast morphology, signal transduction, and integrin-mediated cell adhesion. The protein encoded by this gene is a type II membrane protein which catalyzes the formation of GM3 using lactosylceramide as the substrate. The encoded protein is a member of glycosyltransferase family 29 and may be localized to the Golgi apparatus. Mutation in this gene has been associated with Amish infantile epilepsy syndrome. Transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in adrenal (RPKM 17.6), thyroid (RPKM 16.1) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ST3GAL5 in Genome Data Viewer
    Location:
    2p11.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (85837120..85889034, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (85839198..85891111, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86064243..86116157, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene atonal bHLH transcription factor 8 Neighboring gene microRNA 6071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:86023815-86024558 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:86031662-86031859 Neighboring gene uncharacterized LOC284950 Neighboring gene RN7SK pseudogene 83 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86115293-86115793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11709 Neighboring gene ST3GAL5 antisense RNA 1 (head to head) Neighboring gene uncharacterized LOC124906030

    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. GM3 Synthase Deficiency. Adam MP, et al. , 1993. PMID 37471511
    2. Infantile-onset symptomatic epilepsy syndrome caused by a homozygous loss-of-function mutation of GM3 synthase. Simpson MA, et al. Nat Genet, 2004 Nov. PMID 15502825
    3. Human GM3 synthase: a new mRNA variant encodes an NH2-terminal extended form of the protein. Berselli P, et al. Biochim Biophys Acta, 2006 Jul. PMID 16934889
    4. Molecular mechanism for transcriptional activation of ganglioside GM3 synthase and its function in differentiation of HL-60 cells. Chung TW, et al. Glycobiology, 2005 Mar. PMID 15385432
    5. Ganglioside depletion and EGF responses of human GM3 synthase-deficient fibroblasts. Liu Y, et al. Glycobiology, 2008 Aug. PMID 18480157

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Neural-specific alterations in glycosphingolipid biosynthesis and cell signaling associated with two human ganglioside GM3 synthase deficiency variants.
      Title: Neural-specific alterations in glycosphingolipid biosynthesis and cell signaling associated with two human ganglioside GM3 synthase deficiency variants.
    2. Neurological insights on two siblings with GM3 synthase deficiency due to novel compound heterozygous ST3GAL5 variants.
      Title: Neurological insights on two siblings with GM3 synthase deficiency due to novel compound heterozygous ST3GAL5 variants.
    3. Identification of ST3GAL5 as a prognostic biomarker correlating with CD8(+) T cell exhaustion in clear cell renal cell carcinoma.
      Title: Identification of ST3GAL5 as a prognostic biomarker correlating with CD8(+) T cell exhaustion in clear cell renal cell carcinoma.
    4. GM3 synthase deficiency is a neurodevelopmental disorder with consistent features of profound intellectual disability, choreoathetosis, and deafness.
      Title: ST3GAL5-Related Disorders: A Deficiency in Ganglioside Metabolism and a Genetic Cause of Intellectual Disability and Choreoathetosis.
    5. HEK-293T clones permanently expressing HaloTag-ST3GAL5 carrying each of the five variants were assessed by quantitative PCR, flow cytometry, western blotting and confocal microscopy. Compared with the very mild phenotype of st3gal5 KO mouse models, the results suggest that unknown mechanisms, in addition to the lack of a-b-c-series gangliosides, contribute to the syndrome.
      Title: Total loss of GM3 synthase activity by a normally processed enzyme in a novel variant and in all ST3GAL5 variants reported to cause a distinct congenital disorder of glycosylation.
    6. Since the nineties, mice lacking genes for single glycosyltransferases involved in ganglioside biosynthesis, including ST3GAL5 and B4GALNT1, were created and studied. The resulting phenotypes were frequently mild or very mild, so double knock-out animals were created to effectively study the function of gangliosides
      Title: Diseases of ganglioside biosynthesis: An expanding group of congenital disorders of glycosylation.
    7. While no differences in clinical characteristics were detected in patients possessing the functional promoter haplotypes of ST3GAL5, exophthalmic values were significantly lower in patients with the ST8SIA1 haplotype, which showed a significant increase in promoter activity
      Title: Identification and Functional Characterization of ST3GAL5 and ST8SIA1 Variants in Patients with Thyroid-Associated Ophthalmopathy.
    8. These cases broaden the phenotypic and genetic spectrum of GM3 synthase deficiency due to ST3GAL5 variants. Patients with intellectual disability or furthermore presenting with Rett-like phenotype should be suspected of GM3 synthase deficiency, a disorder of ganglioside biosynthesis.
      Title: GM3 synthase deficiency due to ST3GAL5 variants in two Korean female siblings: Masquerading as Rett syndrome-like phenotype.
    9. Data suggest that ganglioside glycosyltransferases ST3GAL5, ST8SIA1, and B4GALNT1 are S-acylated at conserved cysteine residues located close to cytoplasmic border of their transmembrane domains; ST3Gal-II is acylated at conserved cysteine residue in N-terminal cytoplasmic tail; for B4GALNT1 and ST3Gal-II, dimer formation controls their S-acylation status.
      Title: Ganglioside glycosyltransferases are S-acylated at conserved cysteine residues involved in homodimerisation.
    10. Studied the miRNA expression in human hepatocellular carcinoma cell lines; 13 differentially expressed miRNAs were identified between MHCC97-H and MHCC97-L cells; and the same results were found in clinical samples. Found that ST3GAL5 was the direct target of miR-26a, miR-548l and miR-34a.
      Title: MiRNA expression profiles reveal the involvement of miR-26a, miR-548l and miR-34a in hepatocellular carcinoma progression through regulation of ST3GAL5.
    Submit: New GeneRIF Correction See all GeneRIFs (28)

    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
    GM3 synthase deficiency
    MedGen: C1836824 OMIM: 609056 GeneReviews: GM3 Synthase Deficiency
    		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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    Replication interactions

    Interaction Pubs
    Knockdown of ST3 beta-galactoside alpha-2,3-sialyltransferase 5 (ST3GAL5) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    nucleocapsid gag HIV-1 NC upregulates ST3 beta-galactoside alpha-2,3-sialyltransferase 5 in HEK 293T cells 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables beta-galactoside (CMP) alpha-2,3-sialyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables lactosylceramide alpha-2,3-sialyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lactosylceramide alpha-2,3-sialyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sialyltransferase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ganglioside biosynthetic process IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in glycosphingolipid biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein glycosylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lactosylceramide alpha-2,3-sialyltransferase
    Names
    CMP-NeuAc:lactosylceramide alpha-2,3-sialyltransferase
    GM3 synthase
    ST3 beta-galactoside alpha-23-sialyltransferase 5
    alpha 2,3-sialyltransferase V
    ganglioside GM3 synthase
    sialyltransferase 9 (CMP-NeuAc:lactosylceramide alpha-2,3-sialyltransferase; GM3 synthase)
    NP_001035902.1
    NP_001341152.1
    NP_001341153.1
    NP_001341155.1
    NP_001341156.1
    NP_001341158.1
    NP_001341162.1
    NP_001341163.1
    NP_001341167.1
    NP_001341176.1
    NP_001341177.1
    NP_001350776.1
    NP_003887.3
    XP_047302193.1
    XP_047302194.1
    XP_047302195.1
    XP_047302196.1
    XP_047302197.1
    XP_054200372.1
    XP_054200373.1
    XP_054200374.1
    XP_054200375.1
    XP_054200376.1

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_012807.2 RefSeqGene

      Range
      5044..56914
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001042437.2 → NP_001035902.1  lactosylceramide alpha-2,3-sialyltransferase isoform 2

      See identical proteins and their annotated locations for NP_001035902.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has a novel 5' exon compared to transcript variant 1, and encodes a shorter isoform (2) with a different N-terminus compared to isoform 1.
      Source sequence(s)
      AC105053, AY152815
      Consensus CDS
      CCDS42705.1
      UniProtKB/TrEMBL
      A0A1W2PRC6
      Related
      ENSP00000377397.3, ENST00000393808.8
      Conserved Domains (1) summary
      pfam00777
      Location:121 → 387
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    2. NM_001354223.2 → NP_001341152.1  lactosylceramide alpha-2,3-sialyltransferase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Conserved Domains (1) summary
      pfam00777
      Location:15 → 282
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    3. NM_001354224.2 → NP_001341153.1  lactosylceramide alpha-2,3-sialyltransferase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Conserved Domains (1) summary
      pfam00777
      Location:15 → 282
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    4. NM_001354226.2 → NP_001341155.1  lactosylceramide alpha-2,3-sialyltransferase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Conserved Domains (1) summary
      pfam00777
      Location:15 → 282
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    5. NM_001354227.2 → NP_001341156.1  lactosylceramide alpha-2,3-sialyltransferase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Consensus CDS
      CCDS86856.1
      UniProtKB/TrEMBL
      A0A0S2Z4S6, A0A1W2PRC6
      Conserved Domains (1) summary
      pfam00777
      Location:127 → 382
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    6. NM_001354229.2 → NP_001341158.1  lactosylceramide alpha-2,3-sialyltransferase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Consensus CDS
      CCDS86856.1
      UniProtKB/TrEMBL
      A0A0S2Z4S6, A0A1W2PRC6
      Related
      ENSP00000491853.1, ENST00000638986.1
      Conserved Domains (1) summary
      pfam00777
      Location:127 → 382
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    7. NM_001354233.2 → NP_001341162.1  lactosylceramide alpha-2,3-sialyltransferase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Conserved Domains (1) summary
      pfam00777
      Location:15 → 282
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    8. NM_001354234.1 → NP_001341163.1  lactosylceramide alpha-2,3-sialyltransferase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Conserved Domains (1) summary
      pfam00777
      Location:15 → 282
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    9. NM_001354238.1 → NP_001341167.1  lactosylceramide alpha-2,3-sialyltransferase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC105053, AF105026
      Consensus CDS
      CCDS86856.1
      UniProtKB/TrEMBL
      A0A0S2Z4S6, A0A1W2PRC6
      Related
      ENSP00000377394.1, ENST00000393805.6
      Conserved Domains (1) summary
      pfam00777
      Location:127 → 382
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    10. NM_001354247.1 → NP_001341176.1  lactosylceramide alpha-2,3-sialyltransferase isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Related
      ENST00000640798.1
      Conserved Domains (1) summary
      pfam00777
      Location:1 → 169
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    11. NM_001354248.1 → NP_001341177.1  lactosylceramide alpha-2,3-sialyltransferase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Conserved Domains (1) summary
      pfam00777
      Location:15 → 282
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    12. NM_001363847.1 → NP_001350776.1  lactosylceramide alpha-2,3-sialyltransferase isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC105053
      Consensus CDS
      CCDS86857.1
      UniProtKB/TrEMBL
      A0A0S2Z4Q7, A0A1W2PR45
      Related
      ENSP00000492045.1, ENST00000639119.1
      Conserved Domains (1) summary
      pfam00777
      Location:155 → 357
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    13. NM_003896.4 → NP_003887.3  lactosylceramide alpha-2,3-sialyltransferase isoform 1

      See identical proteins and their annotated locations for NP_003887.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB018356, AC105053, AK001340, CA503200
      Consensus CDS
      CCDS1986.2
      UniProtKB/Swiss-Prot
      B3KM82, D6W5L9, O94902, Q53QU1, Q6NZX4, Q6YFL1, Q9UNP4
      UniProtKB/TrEMBL
      A0A1W2PRC6
      Related
      ENSP00000491316.1, ENST00000638572.2
      Conserved Domains (1) summary
      pfam00777
      Location:144 → 410
      Glyco_transf_29; Glycosyltransferase family 29 (sialyltransferase)

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      85837120..85889034 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446240.1 → XP_047302196.1  lactosylceramide alpha-2,3-sialyltransferase isoform X2

    2. XM_047446238.1 → XP_047302194.1  lactosylceramide alpha-2,3-sialyltransferase isoform X2

    3. XM_047446237.1 → XP_047302193.1  lactosylceramide alpha-2,3-sialyltransferase isoform X1

      UniProtKB/TrEMBL
      A0A0S2Z4S6

    4. XM_047446239.1 → XP_047302195.1  lactosylceramide alpha-2,3-sialyltransferase isoform X2

    5. XM_047446241.1 → XP_047302197.1  lactosylceramide alpha-2,3-sialyltransferase isoform X3

      Related
      ENSP00000492459.1, ENST00000640425.1

    RNA

    1. XR_007084237.1 RNA Sequence

    2. XR_007084231.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      85839198..85891111 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344400.1 → XP_054200375.1  lactosylceramide alpha-2,3-sialyltransferase isoform X2

    2. XM_054344398.1 → XP_054200373.1  lactosylceramide alpha-2,3-sialyltransferase isoform X2

    3. XM_054344397.1 → XP_054200372.1  lactosylceramide alpha-2,3-sialyltransferase isoform X1

    4. XM_054344399.1 → XP_054200374.1  lactosylceramide alpha-2,3-sialyltransferase isoform X2

    5. XM_054344401.1 → XP_054200376.1  lactosylceramide alpha-2,3-sialyltransferase isoform X3

    RNA

    1. XR_008486591.1 RNA Sequence

    2. XR_008486590.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UNP4.4 GenPept UniProtKB/Swiss-Prot:Q9UNP4

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