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    SLC35D1 solute carrier family 35 member D1 [ Homo sapiens (human) ]

    Gene ID: 23169, updated on 2-May-2024

    Summary

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    Official Symbol
    SLC35D1provided by HGNC
    Official Full Name
    solute carrier family 35 member D1provided by HGNC
    Primary source
    HGNC:HGNC:20800
    See related
    Ensembl:ENSG00000116704 MIM:610804; AllianceGenome:HGNC:20800
    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
    SHNKND; UGTREL7
    Summary
    Glycosylation of cellular glycoconjugates occurs in the endoplasmic reticulum (ER) and Golgi compartment, and requires transport of nucleotide sugars from the cytosol into the lumen of the ER and Golgi by specific transporters. The protein encoded by this gene resides in the ER, and transports both UDP-glucuronic acid (UDP-GlcA) and UDP-N-acetylgalactosamine (UDP-GalNAc) from the cytoplasm to the ER lumen. It may participate in glucuronidation and/or chondroitin sulfate biosynthesis. Mutations in this gene are associated with Schneckenbecken dysplasia.[provided by RefSeq, Sep 2009]
    Expression
    Ubiquitous expression in liver (RPKM 14.1), colon (RPKM 11.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p31.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (66972976..67054148, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (66850468..66931662, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (67465033..67519831, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene insulin like 5 Neighboring gene dynein axonemal intermediate chain 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 974 Neighboring gene MIER1 transcriptional regulator Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 975 Neighboring gene MPRA-validated peak274 silencer Neighboring gene MPRA-validated peak275 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:67486227-67487025 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 978 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:67562817-67563435 Neighboring gene small nucleolar RNA SNORA31 Neighboring gene chromosome 1 open reading frame 141 Neighboring gene NANOG hESC enhancer GRCh37_chr1:67602886-67603396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1169 Neighboring gene interleukin 23 receptor Neighboring gene RNA, U6 small nuclear 586, pseudogene

    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
    • 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. A novel SLC35D1 variant causing milder phenotype of Schneckenbecken dysplasia in a large pedigree. Özer L, et al. Am J Med Genet A, 2022 Oct. PMID 35934917
    2. A hypomorphic allele of SLC35D1 results in Schneckenbecken-like dysplasia. Rautengarten C, et al. Hum Mol Genet, 2019 Nov 1. PMID 31423530, Free PMC Article
    3. Identification of loss-of-function mutations of SLC35D1 in patients with Schneckenbecken dysplasia, but not with other severe spondylodysplastic dysplasias group diseases. Furuichi T, et al. J Med Genet, 2009 Aug. PMID 19508970, Free PMC Article
    4. Molecular characterization of human UDP-glucuronic acid/UDP-N-acetylgalactosamine transporter, a novel nucleotide sugar transporter with dual substrate specificity. Muraoka M, et al. FEBS Lett, 2001 Apr 20. PMID 11322953
    5. Fine mapping of the GWAS loci identifies SLC35D1 and IL23R as potential risk genes for leprosy. Li GD, et al. J Dermatol Sci, 2016 Dec. PMID 27712858

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel SLC35D1 variant causing milder phenotype of Schneckenbecken dysplasia in a large pedigree.
      Title: A novel SLC35D1 variant causing milder phenotype of Schneckenbecken dysplasia in a large pedigree.
    2. there is a positive association between the GWAS reported rs3762318 and leprosy, and SLC35D1 and IL23R might be the causal genes
      Title: Fine mapping of the GWAS loci identifies SLC35D1 and IL23R as potential risk genes for leprosy.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. Searched for SLC35D1 mutations, identified four novel mutations in three Schneckenbecken dysplasia families. All mutations result in loss of function. No SLC35D1 mutations were id'd in all patients with other spondylodysplastic dysplasias group diseases.
      Title: Identification of loss-of-function mutations of SLC35D1 in patients with Schneckenbecken dysplasia, but not with other severe spondylodysplastic dysplasias group diseases.
    5. Loss of function mutations cause Schneckenbecken dysplasia, a severe skeletal dysplasia.
      Title: Nucleotide-sugar transporter SLC35D1 is critical to chondroitin sulfate synthesis in cartilage and skeletal development in mouse and human.
    Submit: New GeneRIF Correction

    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
    Schneckenbecken dysplasia
    MedGen: C0432194 OMIM: 269250 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
    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)

    Genotypes

    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

    • KIAA0260, MGC138236

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables UDP-N-acetylgalactosamine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables UDP-N-acetylglucosamine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables UDP-glucuronic acid transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables UDP-glucuronic acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables antiporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables antiporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in UDP-N-acetylgalactosamine transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in UDP-N-acetylglucosamine transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in UDP-glucuronic acid transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nucleotide-sugar transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in pyrimidine nucleotide-sugar transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    nucleotide sugar transporter SLC35D1
    Names
    UDP-GlcA/UDP-GalNAc transporter
    UDP-galactose transporter-related 7
    UDP-galactose transporter-related protein 7
    UDP-glucuronic acid/UDP-N-acetylgalactosamine transporter
    solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1
    solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1

    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_012933.1 RefSeqGene

      Range
      5250..60048
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015139.3 → NP_055954.1  nucleotide sugar transporter SLC35D1

      See identical proteins and their annotated locations for NP_055954.1

      Status: REVIEWED

      Source sequence(s)
      AK289800, BQ001392, BU619019, BU679620, CA391890, D87449
      Consensus CDS
      CCDS636.1
      UniProtKB/Swiss-Prot
      A8K185, B7Z3X2, Q52LU5, Q92548, Q9NTN3
      Related
      ENSP00000235345.5, ENST00000235345.6
      Conserved Domains (1) summary
      COG5070
      Location:49 → 329
      VRG4; Nucleotide-sugar transporter [Carbohydrate transport and metabolism / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      66972976..67054148 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047415662.1 → XP_047271618.1  nucleotide sugar transporter SLC35D1 isoform X3

      UniProtKB/Swiss-Prot
      A8K185, B7Z3X2, Q52LU5, Q92548, Q9NTN3

    2. XM_047415665.1 → XP_047271621.1  nucleotide sugar transporter SLC35D1 isoform X3

      UniProtKB/Swiss-Prot
      A8K185, B7Z3X2, Q52LU5, Q92548, Q9NTN3

    3. XM_047415660.1 → XP_047271616.1  nucleotide sugar transporter SLC35D1 isoform X3

      UniProtKB/Swiss-Prot
      A8K185, B7Z3X2, Q52LU5, Q92548, Q9NTN3

    4. XM_047415671.1 → XP_047271627.1  nucleotide sugar transporter SLC35D1 isoform X5

    5. XM_006710478.3 → XP_006710541.1  nucleotide sugar transporter SLC35D1 isoform X1

      See identical proteins and their annotated locations for XP_006710541.1

      Conserved Domains (1) summary
      COG5070
      Location:49 → 356
      VRG4; Nucleotide-sugar transporter [Carbohydrate transport and metabolism / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

    6. XM_047415659.1 → XP_047271615.1  nucleotide sugar transporter SLC35D1 isoform X2

    7. XM_047415668.1 → XP_047271624.1  nucleotide sugar transporter SLC35D1 isoform X4

    8. XM_047415672.1 → XP_047271628.1  nucleotide sugar transporter SLC35D1 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      66850468..66931662 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335361.1 → XP_054191336.1  nucleotide sugar transporter SLC35D1 isoform X3

      UniProtKB/Swiss-Prot
      A8K185, B7Z3X2, Q52LU5, Q92548, Q9NTN3

    2. XM_054335362.1 → XP_054191337.1  nucleotide sugar transporter SLC35D1 isoform X3

      UniProtKB/Swiss-Prot
      A8K185, B7Z3X2, Q52LU5, Q92548, Q9NTN3

    3. XM_054335360.1 → XP_054191335.1  nucleotide sugar transporter SLC35D1 isoform X3

      UniProtKB/Swiss-Prot
      A8K185, B7Z3X2, Q52LU5, Q92548, Q9NTN3

    4. XM_054335359.1 → XP_054191334.1  nucleotide sugar transporter SLC35D1 isoform X1

    5. XM_054335363.1 → XP_054191338.1  nucleotide sugar transporter SLC35D1 isoform X4

    6. XM_054335364.1 → XP_054191339.1  nucleotide sugar transporter SLC35D1 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NTN3.1 GenPept UniProtKB/Swiss-Prot:Q9NTN3

    Gene LinkOut

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