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    SLC33A1 solute carrier family 33 member 1 [ Homo sapiens (human) ]

    Gene ID: 9197, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SLC33A1provided by HGNC
    Official Full Name
    solute carrier family 33 member 1provided by HGNC
    Primary source
    HGNC:HGNC:95
    See related
    Ensembl:ENSG00000169359 MIM:603690; AllianceGenome:HGNC:95
    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
    AT1; AT-1; ACATN; HPBDS; SPG42; CCHLND
    Summary
    The protein encoded by this gene is required for the formation of O-acetylated (Ac) gangliosides. The encoded protein is predicted to contain 6 to 10 transmembrane domains, and a leucine zipper motif in transmembrane domain III. Defects in this gene have been reported to cause spastic paraplegia autosomal dominant type 42 (SPG42) in one Chinese family, but not in similar patients of European descent. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]
    Expression
    Ubiquitous expression in thyroid (RPKM 20.1), duodenum (RPKM 13.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC33A1 in Genome Data Viewer
    Location:
    3q25.31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (155821024..155854427, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (158595660..158629057, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (155538813..155572216, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L7a pseudogene 24 Neighboring gene chromosome 3 open reading frame 33 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:155507600-155507774 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:155508647-155509846 Neighboring gene MPRA-validated peak4874 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20722 Neighboring gene uncharacterized LOC105374174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:155588473-155589232 Neighboring gene guanine monophosphate synthase Neighboring gene ReSE screen-validated silencer GRCh37_chr3:155626010-155626276

    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 SLC33A1 cause a lethal autosomal-recessive disorder with congenital cataracts, hearing loss, and low serum copper and ceruloplasmin. Huppke P, et al. Am J Hum Genet, 2012 Jan 13. PMID 22243965, Free PMC Article
    2. Huppke-Brendel Syndrome. Adam MP, et al. , 1993. PMID 31194315
    3. A total of 220 patients with autosomal dominant spastic paraplegia do not display mutations in the SLC33A1 gene (SPG42). Schlipf NA, et al. Eur J Hum Genet, 2010 Sep. PMID 20461110, Free PMC Article
    4. Prenatal diagnosis of autosomal dominant hereditary spastic paraplegia (SPG42) caused by SLC33A1 mutation in a Chinese kindred. Lin P, et al. Prenat Diagn, 2010 May. PMID 20306460
    5. Deficient import of acetyl-CoA into the ER lumen causes neurodegeneration and propensity to infections, inflammation, and cancer. Peng Y, et al. J Neurosci, 2014 May 14. PMID 24828632, Free PMC Article

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1.
      Title: Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1.
    2. Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway.
      Title: Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway.
    3. results indicate that increased expression of AT-1 can cause an autistic-like phenotype by affecting key neuronal metabolic pathways.
      Title: Increased expression of AT-1/SLC33A1 causes an autistic-like phenotype in mice by affecting dendritic branching and spine formation.
    4. SLC33A1 can negatively regulate BMP signaling.
      Title: Identification and functional analysis of a SLC33A1: c.339T>G (p.Ser113Arg) variant in the original SPG42 family.
    5. IRE1/XBP1 controls the induction of autophagy/ERAD(II) during the unfolded protein response by activating the ER membrane transporter SLC33A1/AT-1
      Title: SLC33A1/AT-1 protein regulates the induction of autophagy downstream of IRE1/XBP1 pathway.
    6. Homozygosity mapping displayed a region of commonality among three families at chromosome 3q25. Deep sequencing and conventional sequencing disclosed homozygous or compound heterozygous mutations for all affected subjects in SLC33A1.
      Title: Mutations in SLC33A1 cause a lethal autosomal-recessive disorder with congenital cataracts, hearing loss, and low serum copper and ceruloplasmin.
    7. translocates acetyl-CoA into the ER lumen and is essential for cell viability
      Title: AT-1 is the ER membrane acetyl-CoA transporter and is essential for cell viability.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: A total of 220 patients with autosomal dominant spastic paraplegia do not display mutations in the SLC33A1 gene (SPG42).
    9. A missense mutation in SLC33A1 causes autosomal-dominant spastic paraplegia.
      Title: A missense mutation in SLC33A1, which encodes the acetyl-CoA transporter, causes autosomal-dominant spastic paraplegia (SPG42).
    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
    Hereditary spastic paraplegia 42
    MedGen: C2675528 OMIM: 612539 GeneReviews: Not available
    		Compare labs
    Huppke-Brendel syndrome
    MedGen: C4751114 OMIM: 614482 GeneReviews: Huppke-Brendel Syndrome
    		Compare labs

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables acetyl-CoA transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables acetyl-CoA transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in acetyl-CoA transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    acetyl-coenzyme A transporter 1
    Names
    solute carrier family 33 (acetyl-CoA 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_023365.2 RefSeqGene

      Range
      5000..38403
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001190992.2 → NP_001177921.1  acetyl-coenzyme A transporter 1 isoform 1

      See identical proteins and their annotated locations for NP_001177921.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC104472, BC014416
      Consensus CDS
      CCDS3173.1
      UniProtKB/Swiss-Prot
      B2R5Q2, D3DNK4, O00400
      Related
      ENSP00000352456.3, ENST00000359479.7
      Conserved Domains (1) summary
      TIGR00901
      Location:86 → 458
      2A0125; AmpG-like permease

    2. NM_001363883.1 → NP_001350812.1  acetyl-coenzyme A transporter 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC104472
      Consensus CDS
      CCDS87159.1
      UniProtKB/TrEMBL
      A0A2R8YF57
      Related
      ENSP00000494846.1, ENST00000646424.1
      Conserved Domains (1) summary
      cl21472
      Location:85 → 442
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

    3. NM_004733.4 → NP_004724.1  acetyl-coenzyme A transporter 1 isoform 1

      See identical proteins and their annotated locations for NP_004724.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC104472, D88152
      Consensus CDS
      CCDS3173.1
      UniProtKB/Swiss-Prot
      B2R5Q2, D3DNK4, O00400
      Related
      ENSP00000496241.1, ENST00000643144.2
      Conserved Domains (1) summary
      TIGR00901
      Location:86 → 458
      2A0125; AmpG-like permease

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      155821024..155854427 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007464.2 → XP_016862953.1  acetyl-coenzyme A transporter 1 isoform X7

      UniProtKB/TrEMBL
      H7C562

    2. XM_011513311.4 → XP_011511613.1  acetyl-coenzyme A transporter 1 isoform X1

      Conserved Domains (1) summary
      cl21472
      Location:85 → 443
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

    3. XM_017007463.2 → XP_016862952.1  acetyl-coenzyme A transporter 1 isoform X4

    4. XM_047449195.1 → XP_047305151.1  acetyl-coenzyme A transporter 1 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YF57

    5. XM_047449200.1 → XP_047305156.1  acetyl-coenzyme A transporter 1 isoform X7

    6. XM_047449194.1 → XP_047305150.1  acetyl-coenzyme A transporter 1 isoform X1

    7. XM_047449197.1 → XP_047305153.1  acetyl-coenzyme A transporter 1 isoform X4

    8. XM_047449196.1 → XP_047305152.1  acetyl-coenzyme A transporter 1 isoform X3

    9. XM_047449199.1 → XP_047305155.1  acetyl-coenzyme A transporter 1 isoform X6

      UniProtKB/TrEMBL
      H7C532
      Related
      ENSP00000418847.2, ENST00000468581.2

    10. XM_047449198.1 → XP_047305154.1  acetyl-coenzyme A transporter 1 isoform X5

      UniProtKB/TrEMBL
      A0A2R8Y5I5
      Related
      ENSP00000494476.1, ENST00000644094.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      158595660..158629057 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348373.1 → XP_054204348.1  acetyl-coenzyme A transporter 1 isoform X7

    2. XM_054348366.1 → XP_054204341.1  acetyl-coenzyme A transporter 1 isoform X1

    3. XM_054348370.1 → XP_054204345.1  acetyl-coenzyme A transporter 1 isoform X4

    4. XM_054348368.1 → XP_054204343.1  acetyl-coenzyme A transporter 1 isoform X2

      UniProtKB/TrEMBL
      A0A2R8YF57

    5. XM_054348374.1 → XP_054204349.1  acetyl-coenzyme A transporter 1 isoform X7

    6. XM_054348367.1 → XP_054204342.1  acetyl-coenzyme A transporter 1 isoform X1

    7. XM_054348369.1 → XP_054204344.1  acetyl-coenzyme A transporter 1 isoform X3

    8. XM_054348372.1 → XP_054204347.1  acetyl-coenzyme A transporter 1 isoform X6

      UniProtKB/TrEMBL
      H7C532

    9. XM_054348371.1 → XP_054204346.1  acetyl-coenzyme A transporter 1 isoform X5

      UniProtKB/TrEMBL
      A0A2R8Y5I5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O00400.1 GenPept UniProtKB/Swiss-Prot:O00400

    Gene LinkOut

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

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