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    SLC35A1 solute carrier family 35 member A1 [ Homo sapiens (human) ]

    Gene ID: 10559, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SLC35A1provided by HGNC
    Official Full Name
    solute carrier family 35 member A1provided by HGNC
    Primary source
    HGNC:HGNC:11021
    See related
    Ensembl:ENSG00000164414 MIM:605634; AllianceGenome:HGNC:11021
    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
    CST; hCST; CDG2F; CMPST
    Summary
    The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]
    Expression
    Ubiquitous expression in colon (RPKM 23.8), lung (RPKM 21.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC35A1 in Genome Data Viewer
    Location:
    6q15
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (87472974..87512336)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (88681733..88721067)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (88182692..88222054)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 206 Neighboring gene ST13, Hsp70 interacting protein pseudogene 16 Neighboring gene uncharacterized LOC124901357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:88182339-88183245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24796 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:88193750-88194949 Neighboring gene RNA, U6 small nuclear 444, pseudogene Neighboring gene arginyl-tRNA synthetase 2, mitochondrial Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24797 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:88298835-88299796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:88301170-88301670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:88301671-88302171 Neighboring gene NANOG hESC enhancer GRCh37_chr6:88313800-88314301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:88323459-88323960 Neighboring gene origin recognition complex subunit 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:88349062-88349578 Neighboring gene MPRA-validated peak5943 silencer Neighboring gene akirin 2

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A three-pocket model for substrate coordination and selectivity by the nucleotide sugar transporters SLC35A1 and SLC35A2.
      Title: A three-pocket model for substrate coordination and selectivity by the nucleotide sugar transporters SLC35A1 and SLC35A2.
    2. Knockout of the CMP-Sialic Acid Transporter SLC35A1 in Human Cell Lines Increases Transduction Efficiency of Adeno-Associated Virus 9: Implications for Gene Therapy Potency Assays.
      Title: Knockout of the CMP-Sialic Acid Transporter SLC35A1 in Human Cell Lines Increases Transduction Efficiency of Adeno-Associated Virus 9: Implications for Gene Therapy Potency Assays.
    3. The promiscuous binding pocket of SLC35A1 ensures redundant transport of CDP-ribitol to the Golgi.
      Title: The promiscuous binding pocket of SLC35A1 ensures redundant transport of CDP-ribitol to the Golgi.
    4. Slc35a1 deficiency causes thrombocytopenia due to impaired megakaryocytopoiesis and excessive platelet clearance in the liver.
      Title: Slc35a1 deficiency causes thrombocytopenia due to impaired megakaryocytopoiesis and excessive platelet clearance in the liver.
    5. Novel Insights into Selected Disease-Causing Mutations within the SLC35A1 Gene Encoding the CMP-Sialic Acid Transporter.
      Title: Novel Insights into Selected Disease-Causing Mutations within the SLC35A1 Gene Encoding the CMP-Sialic Acid Transporter.
    6. Data indicate a congenital deficiency in solute carrier family 35 (CMP-sialic acid transporter), member A1 (SLC35A1) mutation in two siblings born to consanguineous parents and who displayed moderate macrothrombocytopenia.
      Title: A mutation in the gene coding for the sialic acid transporter SLC35A1 is required for platelet life span but not proplatelet formation.
    7. We performed exome sequencing on an individual with a profound neurological presentation and identified rare compound heterozygous mutations, p.Thr156Arg and p.Glu196Lys, in the CMP-sialic acid transporter, SLC35A1. Patient primary fibroblasts and serum showed a considerable decrease in the amount of N- and O-glycans terminating in sialic acid
      Title: Encephalopathy caused by novel mutations in the CMP-sialic acid transporter, SLC35A1.
    8. the SLC35A1 generates additional isoforms through alternative splicing.
      Title: A functional splice variant of the human Golgi CMP-sialic acid transporter.
    9. SLC35A1-deficient cells lack of alpha-dystroglycan O-mannosylation, ligand binding and incorporation of sialic acids.
      Title: Disease mutations in CMP-sialic acid transporter SLC35A1 result in abnormal α-dystroglycan O-mannosylation, independent from sialic acid.
    10. We confirm an autosomal recessive, generalized sialylation defect due to mutations in SLC35A1
      Title: Intellectual disability and bleeding diathesis due to deficient CMP--sialic acid transport.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • FLJ76955

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables CMP-N-acetylneuraminate transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables CMP-N-acetylneuraminate transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables CMP-N-acetylneuraminate transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables antiporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in CMP-N-acetylneuraminate biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in CMP-N-acetylneuraminate transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in CMP-N-acetylneuraminate transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in CMP-N-acetylneuraminate transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in carbohydrate metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in protein modification process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    CMP-sialic acid transporter
    Names
    CMP-SA-Tr
    CMP-Sia-Tr
    mutated CMP-sialic acid transporter A1
    solute carrier family 35 (CMP-sialic acid transporter), member 1
    solute carrier family 35 (CMP-sialic acid transporter), member A1
    solute carrier family 35 (UDP-galactose transporter), member 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.

    Genomic

    1. NG_016207.1 RefSeqGene

      Range
      5050..44412
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001168398.2 → NP_001161870.1  CMP-sialic acid transporter isoform b

      See identical proteins and their annotated locations for NP_001161870.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AJ851888, CB242593, D87969, DA210713
      Consensus CDS
      CCDS55043.1
      UniProtKB/Swiss-Prot
      P78382
      Related
      ENSP00000358569.3, ENST00000369556.7
      Conserved Domains (1) summary
      pfam04142
      Location:8 → 255
      Nuc_sug_transp; Nucleotide-sugar transporter

    2. NM_006416.5 → NP_006407.1  CMP-sialic acid transporter isoform a

      See identical proteins and their annotated locations for NP_006407.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      BC017807, BG699364, CB242593, DB095595
      Consensus CDS
      CCDS5010.1
      UniProtKB/Swiss-Prot
      P78382, Q5W1L8
      Related
      ENSP00000358565.4, ENST00000369552.9
      Conserved Domains (1) summary
      pfam04142
      Location:8 → 314
      Nuc_sug_transp; Nucleotide-sugar transporter

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      87472974..87512336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      88681733..88721067
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P78382.1 GenPept UniProtKB/Swiss-Prot:P78382

    Gene LinkOut

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