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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
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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

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