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

Gene ID: 55343, updated on 2-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
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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 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)

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

  • 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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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

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