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

Gene ID: 10559, updated on 11-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (87472974..87512336)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (88681733..88721067)
105.20220307 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
  • 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. 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. Banning A, et al. Cells, 2021 May 19. PMID 34069698, Free PMC Article
  2. Novel Insights into Selected Disease-Causing Mutations within the SLC35A1 Gene Encoding the CMP-Sialic Acid Transporter. Szulc B, et al. Int J Mol Sci, 2020 Dec 30. PMID 33396746, Free PMC Article
  3. Slc35a1 deficiency causes thrombocytopenia due to impaired megakaryocytopoiesis and excessive platelet clearance in the liver. Ma X, et al. Haematologica, 2021 Mar 1. PMID 32303557, Free PMC Article
  4. A mutation in the gene coding for the sialic acid transporter SLC35A1 is required for platelet life span but not proplatelet formation. Kauskot A, et al. Haematologica, 2018 Dec. PMID 30115659, Free PMC Article
  5. Encephalopathy caused by novel mutations in the CMP-sialic acid transporter, SLC35A1. Ng BG, et al. Am J Med Genet A, 2017 Nov. PMID 28856833, Free PMC Article

See all (42) citations in PubMed

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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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
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)

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

  • 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 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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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_2023_10

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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