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    SLC35C1 solute carrier family 35 member C1 [ Homo sapiens (human) ]

    Gene ID: 55343, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SLC35C1provided by HGNC
    Official Full Name
    solute carrier family 35 member C1provided by HGNC
    Primary source
    HGNC:HGNC:20197
    See related
    Ensembl:ENSG00000181830 MIM:605881; AllianceGenome:HGNC:20197
    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
    CDG2C; FUCT1
    Summary
    This gene encodes a GDP-fucose transporter that is found in the Golgi apparatus. Mutations in this gene result in congenital disorder of glycosylation type IIc. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]
    Expression
    Ubiquitous expression in esophagus (RPKM 13.7), small intestine (RPKM 9.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Try the new Transcript table

    Genomic context

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    See SLC35C1 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (45804079..45813016)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (45960045..45968982)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45825630..45834567)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45777387-45778100 Neighboring gene long intergenic non-protein coding RNA 2690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45792675-45793176 Neighboring gene long intergenic non-protein coding RNA 2716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4669 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45869217-45869738 Neighboring gene Sharpr-MPRA regulatory region 9087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4671 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:45880664-45881863 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:45882374-45883573 Neighboring gene cryptochrome circadian regulator 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:45887051-45887552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3290 Neighboring gene mitogen-activated protein kinase 8 interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45917073-45917944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45917945-45918814 Neighboring gene uncharacterized LOC124902668 Neighboring gene Sharpr-MPRA regulatory region 31

    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. Mutations in the SLC35C1 gene, contributing to significant differences in fucosylation patterns, may underlie the diverse phenotypic manifestations observed in leukocyte adhesion deficiency type II patients. Skurska E, et al. Int J Biochem Cell Biol, 2024 Aug. PMID 38843991
    2. The gene defective in leukocyte adhesion deficiency II encodes a putative GDP-fucose transporter. Lühn K, et al. Nat Genet, 2001 May. PMID 11326279
    3. Congenital disorders of glycosylation with defective fucosylation. Hüllen A, et al. J Inherit Metab Dis, 2021 Nov. PMID 34389986
    4. Insights into leukocyte adhesion deficiency type 2 from a novel mutation in the GDP-fucose transporter gene. Hidalgo A, et al. Blood, 2003 Mar 1. PMID 12406889
    5. Leukocyte adhesion deficiency II patients with a dual defect of the GDP-fucose transporter. Helmus Y, et al. Blood, 2006 May 15. PMID 16455955

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mutations in the SLC35C1 gene, contributing to significant differences in fucosylation patterns, may underlie the diverse phenotypic manifestations observed in leukocyte adhesion deficiency type II patients.
      Title: Mutations in the SLC35C1 gene, contributing to significant differences in fucosylation patterns, may underlie the diverse phenotypic manifestations observed in leukocyte adhesion deficiency type II patients.
    2. In vivo evidence for GDP-fucose transport in the absence of transporter SLC35C1 and putative transporter SLC35C2.
      Title: In vivo evidence for GDP-fucose transport in the absence of transporter SLC35C1 and putative transporter SLC35C2.
    3. Congenital disorders of glycosylation with defective fucosylation.
      Title: Congenital disorders of glycosylation with defective fucosylation.
    4. Down-regulation of SLC35C1 induces colon cancer through over-activating Wnt pathway.
      Title: Down-regulation of SLC35C1 induces colon cancer through over-activating Wnt pathway.
    5. two Turkish siblings with a novel mutation in GDP-fucose transporter and features of congenital disorder of glycosylation IIc
      Title: A novel mutation in leukocyte adhesion deficiency type II/CDGIIc.
    6. Fx enzyme and GDP-L-Fuc Tr overexpression in the tumur tissue of colorectal cancer (CRC) patients suggests that GDP-L-Fuc transport to the Golgi apparatus may be an important factor associated with increased alpha(1,6)fucosylation in CRC.
      Title: FX enzyme and GDP-L-Fuc transporter expression in colorectal cancer.
    7. In the rare LAD-II disease, the fucosylation of selectin ligands is disturbed, caused by mutations in SLC35C1, the gene that encodes a GDP-fucose transporter of the Golgi system. (Review)
      Title: Hematologically important mutations: leukocyte adhesion deficiency (first update).
    8. the conserved glycine residues at positions 180 and 277 of SLC35C1 have significant impacts on lectin binding
      Title: Identification of functional elements of the GDP-fucose transporter SLC35C1 using a novel Chinese hamster ovary mutant.
    9. the upregulation of GDP-Fuc Tr plays a pivotal role in increased fucosylation in hepatocellular carcinoma
      Title: A high expression of GDP-fucose transporter in hepatocellular carcinoma is a key factor for increases in fucosylation.
    10. In the GDP-fucose transporter a new single nucleotide deletion produced an open-reading frame shift & polypeptide truncation. Overexpression of the mutant protein in fibroblasts did not rescue fucosylation. The deletion ablated transporter activity.
      Title: Insights into leukocyte adhesion deficiency type 2 from a novel mutation in the GDP-fucose transporter gene.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    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

    • FLJ11320, FLJ14841

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GDP-fucose transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GDP-fucose transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GDP-fucose transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables antiporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in GDP-L-fucose biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in GDP-fucose import into Golgi lumen IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in GDP-fucose import into Golgi lumen IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in lipid glycosylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein O-linked fucosylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    GDP-fucose transporter 1
    Names
    solute carrier family 35 (GDP-fucose transporter), member C1

    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_009875.1 RefSeqGene

      Range
      5001..13945
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_107

    mRNA and Protein(s)

    1. NM_001145265.2 → NP_001138737.1  GDP-fucose transporter 1 isoform b

      See identical proteins and their annotated locations for NP_001138737.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' splice pattern and downstream start codon, compared to variant 1. The resulting isoform (b) has a shorter N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AK002182, BC001427
      Consensus CDS
      CCDS44575.1
      UniProtKB/Swiss-Prot
      Q96A29
      Related
      ENSP00000412408.2, ENST00000442528.2
      Conserved Domains (1) summary
      pfam03151
      Location:26 → 207
      TPT; Triose-phosphate Transporter family

    2. NM_001145266.2 → NP_001138738.1  GDP-fucose transporter 1 isoform b

      See identical proteins and their annotated locations for NP_001138738.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' splice pattern and downstream start codon, compared to variant 1. The resulting isoform (b) has a shorter N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AC044839
      Consensus CDS
      CCDS44575.1
      UniProtKB/Swiss-Prot
      Q96A29
      Related
      ENSP00000432145.2, ENST00000526817.2
      Conserved Domains (1) summary
      pfam03151
      Location:26 → 207
      TPT; Triose-phosphate Transporter family

    3. NM_001425155.1 → NP_001412084.1  GDP-fucose transporter 1 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC044839
      UniProtKB/Swiss-Prot
      B2RDB2, Q96A29, Q9BV76, Q9NUJ8
      UniProtKB/TrEMBL
      B3KQH0

    4. NM_001425156.1 → NP_001412085.1  GDP-fucose transporter 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC044839

    5. NM_018389.5 → NP_060859.4  GDP-fucose transporter 1 isoform a

      See identical proteins and their annotated locations for NP_060859.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AK074929, AK315473, BC001427
      Consensus CDS
      CCDS7914.1
      UniProtKB/Swiss-Prot
      B2RDB2, Q96A29, Q9BV76, Q9NUJ8
      UniProtKB/TrEMBL
      B3KQH0
      Related
      ENSP00000313318.3, ENST00000314134.4
      Conserved Domains (1) summary
      cl23754
      Location:42 → 183
      EamA; EamA-like transporter family

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      45804079..45813016
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520203.4 → XP_011518505.1  GDP-fucose transporter 1 isoform X2

      UniProtKB/TrEMBL
      E9PPI4
      Related
      ENSP00000432669.1, ENST00000530471.1
      Conserved Domains (1) summary
      pfam03151
      Location:39 → 179
      TPT; Triose-phosphate Transporter family

    2. XM_011520202.3 → XP_011518504.1  GDP-fucose transporter 1 isoform X1

      See identical proteins and their annotated locations for XP_011518504.1

      Conserved Domains (1) summary
      cl22888
      Location:89 → 170
      EamA; EamA-like transporter family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      45960045..45968982
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369298.1 → XP_054225273.1  GDP-fucose transporter 1 isoform X2

    2. XM_054369297.1 → XP_054225272.1  GDP-fucose transporter 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96A29.1 GenPept UniProtKB/Swiss-Prot:Q96A29

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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