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SLC35A3 solute carrier family 35 member A3 [ Homo sapiens (human) ]

Gene ID: 23443, updated on 11-Apr-2024

Summary

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Official Symbol
SLC35A3provided by HGNC
Official Full Name
solute carrier family 35 member A3provided by HGNC
Primary source
HGNC:HGNC:11023
See related
Ensembl:ENSG00000117620 MIM:605632; AllianceGenome:HGNC:11023
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
AMRS
Summary
This gene encodes a UDP-N-acetylglucosamine transporter found in the golgi apparatus membrane. In cattle, a missense mutation in this gene causes complex vertebral malformation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
Expression
Broad expression in colon (RPKM 21.3), duodenum (RPKM 16.3) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
1p21.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (99969996..100035634)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (99818116..99883750)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (100435552..100501190)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100315063-100316037 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100316038-100317011 Neighboring gene ribosomal protein L39 pseudogene 9 Neighboring gene amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase Neighboring gene uncharacterized LOC124904230 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100415895-100416089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1365 Neighboring gene RNA, U6 small nuclear 750, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100471652-100472152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100472153-100472653 Neighboring gene RNA, U6 small nuclear 1318, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100503123-100503725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100514024-100514739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1370 Neighboring gene major facilitator superfamily domain containing 14A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1372 Neighboring gene SAS-6 centriolar assembly protein Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100578889-100579078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1373 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100598108-100598271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100598267-100598869

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. Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3. Markolin P, et al. Genomics, 2021 Mar. PMID 33418078
  2. Biosynthesis of GlcNAc-rich N- and O-glycans in the Golgi apparatus does not require the nucleotide sugar transporter SLC35A3. Szulc B, et al. J Biol Chem, 2020 Nov 27. PMID 32938718, Free PMC Article
  3. A human case of SLC35A3-related skeletal dysplasia. Edmondson AC, et al. Am J Med Genet A, 2017 Oct. PMID 28777481
  4. Recessive mutations in SLC35A3 cause early onset epileptic encephalopathy with skeletal defects. Marini C, et al. Am J Med Genet A, 2017 Apr. PMID 28328131
  5. Mutations in SLC35A3 cause autism spectrum disorder, epilepsy and arthrogryposis. Edvardson S, et al. J Med Genet, 2013 Nov. PMID 24031089

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Colorectal cancer with low SLC35A3 is associated with immune infiltrates and poor prognosis.
    Title: Colorectal cancer with low SLC35A3 is associated with immune infiltrates and poor prognosis.
  2. Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3.
    Title: Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3.
  3. Serum bikunin isoforms in congenital disorders of glycosylation and linkeropathies.
    Title: Serum bikunin isoforms in congenital disorders of glycosylation and linkeropathies.
  4. Biosynthesis of GlcNAc-rich N- and O-glycans in the Golgi apparatus does not require the nucleotide sugar transporter SLC35A3.
    Title: Biosynthesis of GlcNAc-rich N- and O-glycans in the Golgi apparatus does not require the nucleotide sugar transporter SLC35A3.
  5. SLC35A3 missense homozygous mutation is associated with skeletal dysplasia.
    Title: A human case of SLC35A3-related skeletal dysplasia.
  6. Recessive mutations in SLC35A3 caused early onset epileptic encephalopathy with skeletal defects in two siblings in an Italian non-consanguineous family.
    Title: Recessive mutations in SLC35A3 cause early onset epileptic encephalopathy with skeletal defects.
  7. UDP-galactose (SLC35A2) and UDP-N-acetylglucosamine (SLC35A3) Transporters Form Glycosylation-related Complexes with Mannoside Acetylglucosaminyltransferases (Mgats).
    Title: UDP-galactose (SLC35A2) and UDP-N-acetylglucosamine (SLC35A3) Transporters Form Glycosylation-related Complexes with Mannoside Acetylglucosaminyltransferases (Mgats).
  8. Identified deleterious mutations in SLC35A3 in eight patients from a large kindred, who suffered from autism spectrum disorder, arthrogryposis and epilepsy.
    Title: Mutations in SLC35A3 cause autism spectrum disorder, epilepsy and arthrogryposis.
  9. The data further supports the hypothesis that UGT and NGT cooperate in the UDP-Gal delivery for glycosyltransferases located in the Golgi apparatus.
    Title: UDP-Gal/UDP-GlcNAc chimeric transporter complements mutation defect in mammalian cells deficient in UDP-Gal transporter.
  10. A mutation in the SLC35A3 gene is associated with vertebral malformations in cattle. A missense mutation likely effects signal transduction which relies on glycosylation.
    Title: A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation.
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

Associated conditions

Description Tests
Autism spectrum disorder - epilepsy - arthrogryposis syndrome
MedGen: C3809910 OMIM: 615553 GeneReviews: Not available
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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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env Mannose-containing, N-linked oligosaccharide side-chains of HIV-1 gp41 are involved in the initial stage of infection by HIV-1; glycosylation inhibitors block virus-cell and cell-cell fusion and release of the virions PubMed

Go to the HIV-1, Human Interaction Database

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

  • DKFZp781P1297

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables UDP-N-acetylglucosamine transmembrane transporter activity TAS
Traceable Author Statement
more info
  
enables UDP-galactose transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in UDP-N-acetylglucosamine metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in UDP-N-acetylglucosamine transmembrane transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in UDP-galactose transmembrane import into Golgi lumen IBA
Inferred from Biological aspect of Ancestor
more info
  
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 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
UDP-N-acetylglucosamine transporter
Names
golgi UDP-GlcNAc transporter
solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3
solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3

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_033857.2 RefSeqGene

    Range
    5002..70640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001271684.2 → NP_001258613.1  UDP-N-acetylglucosamine transporter isoform 2

    See identical proteins and their annotated locations for NP_001258613.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two exons in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC093019, AC118553, AV698459, BC005136, CR749816
    Consensus CDS
    CCDS60205.1
    UniProtKB/TrEMBL
    A0A1W2PQD6
    Related
    ENSP00000491145.1, ENST00000638336.1
    Conserved Domains (1) summary
    pfam04142
    Location:4 → 220
    Nuc_sug_transp; Nucleotide-sugar transporter

  2. NM_001271685.2 → NP_001258614.1  UDP-N-acetylglucosamine transporter isoform 3

    See identical proteins and their annotated locations for NP_001258614.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' exon structure, which introduces an upstream start codon, compared to variant 1. It encodes isoform 3, which has a longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AC093019, AC118553, CR749816
    Consensus CDS
    CCDS60204.1
    UniProtKB/TrEMBL
    A0A1W2PQH2
    Related
    ENSP00000359172.1, ENST00000370153.6
    Conserved Domains (2) summary
    TIGR00803
    Location:128 → 354
    nst; UDP-galactose transporter
    pfam04142
    Location:46 → 355
    Nuc_sug_transp; Nucleotide-sugar transporter

  3. NM_012243.3 → NP_036375.1  UDP-N-acetylglucosamine transporter isoform 1

    See identical proteins and their annotated locations for NP_036375.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
    Source sequence(s)
    AB021981, AC093019, AC118553, CR749816
    Consensus CDS
    CCDS762.1
    UniProtKB/Swiss-Prot
    A8K3F8, D3DT54, Q68CR2, Q9BSB7, Q9Y2D2
    UniProtKB/TrEMBL
    A0A1W2PQH2
    Related
    ENSP00000433849.1, ENST00000533028.8
    Conserved Domains (2) summary
    TIGR00803
    Location:86 → 312
    nst; UDP-galactose transporter
    pfam04142
    Location:4 → 313
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    99969996..100035634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005270691.6 → XP_005270748.1  UDP-N-acetylglucosamine transporter isoform X2

    See identical proteins and their annotated locations for XP_005270748.1

    UniProtKB/Swiss-Prot
    A8K3F8, D3DT54, Q68CR2, Q9BSB7, Q9Y2D2
    UniProtKB/TrEMBL
    A0A1W2PQH2
    Related
    ENSP00000414947.2, ENST00000427993.7
    Conserved Domains (2) summary
    TIGR00803
    Location:86 → 312
    nst; UDP-galactose transporter
    pfam04142
    Location:4 → 313
    Nuc_sug_transp; Nucleotide-sugar transporter

  2. XM_017000870.3 → XP_016856359.1  UDP-N-acetylglucosamine transporter isoform X5

    UniProtKB/TrEMBL
    A0A1W2PRN3, A0A1W2PSD1
    Related
    ENSP00000492801.1, ENST00000640715.1

  3. XM_017000869.3 → XP_016856358.1  UDP-N-acetylglucosamine transporter isoform X4

    UniProtKB/TrEMBL
    A0A1W2PRT7, A0A1W2PS45
    Related
    ENSP00000492771.1, ENST00000640732.1

  4. XM_017000871.3 → XP_016856360.1  UDP-N-acetylglucosamine transporter isoform X7

    UniProtKB/TrEMBL
    A0A1W2PQL8, A0A1W2PRN3
    Related
    ENSP00000492169.1, ENST00000639221.1

  5. XM_047416587.1 → XP_047272543.1  UDP-N-acetylglucosamine transporter isoform X9

  6. XM_047416588.1 → XP_047272544.1  UDP-N-acetylglucosamine transporter isoform X10

    UniProtKB/TrEMBL
    A0A1W2PR66
    Related
    ENSP00000492128.1, ENST00000640726.1

  7. XM_011541137.4 → XP_011539439.1  UDP-N-acetylglucosamine transporter isoform X3

    UniProtKB/TrEMBL
    A0A1W2PRN3
    Conserved Domains (1) summary
    TIGR00803
    Location:128 → 293
    nst; UDP-galactose transporter

  8. XM_011541138.4 → XP_011539440.1  UDP-N-acetylglucosamine transporter isoform X6

    UniProtKB/TrEMBL
    A0A1W2PQD6
    Conserved Domains (1) summary
    cl23754
    Location:128 → 258
    EamA; EamA-like transporter family

  9. XM_011541135.4 → XP_011539437.1  UDP-N-acetylglucosamine transporter isoform X1

    Conserved Domains (2) summary
    TIGR00803
    Location:128 → 313
    nst; UDP-galactose transporter
    pfam04142
    Location:46 → 314
    Nuc_sug_transp; Nucleotide-sugar transporter

  10. XM_047416586.1 → XP_047272542.1  UDP-N-acetylglucosamine transporter isoform X8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    99818116..99883750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335691.1 → XP_054191666.1  UDP-N-acetylglucosamine transporter isoform X2

    UniProtKB/Swiss-Prot
    A8K3F8, D3DT54, Q68CR2, Q9BSB7, Q9Y2D2

  2. XM_054335694.1 → XP_054191669.1  UDP-N-acetylglucosamine transporter isoform X5

    UniProtKB/TrEMBL
    A0A1W2PSD1

  3. XM_054335693.1 → XP_054191668.1  UDP-N-acetylglucosamine transporter isoform X4

    UniProtKB/TrEMBL
    A0A1W2PRT7

  4. XM_054335696.1 → XP_054191671.1  UDP-N-acetylglucosamine transporter isoform X7

    UniProtKB/TrEMBL
    A0A1W2PQL8

  5. XM_054335698.1 → XP_054191673.1  UDP-N-acetylglucosamine transporter isoform X9

  6. XM_054335699.1 → XP_054191674.1  UDP-N-acetylglucosamine transporter isoform X10

    UniProtKB/TrEMBL
    A0A1W2PR66

  7. XM_054335692.1 → XP_054191667.1  UDP-N-acetylglucosamine transporter isoform X3

  8. XM_054335695.1 → XP_054191670.1  UDP-N-acetylglucosamine transporter isoform X6

  9. XM_054335690.1 → XP_054191665.1  UDP-N-acetylglucosamine transporter isoform X1

  10. XM_054335697.1 → XP_054191672.1  UDP-N-acetylglucosamine transporter isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2D2.1 GenPept UniProtKB/Swiss-Prot:Q9Y2D2

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