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

Gene ID: 23169, updated on 2-Nov-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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See SLC35D1 in Genome Data Viewer
Location:
1p31.3
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (66972976..67054148, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (66850468..66931662, complement)
RS_2024_09 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 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 (21) 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
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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_2024_08

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

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