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    ATL1 atlastin GTPase 1 [ Homo sapiens (human) ]

    Gene ID: 51062, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ATL1provided by HGNC
    Official Full Name
    atlastin GTPase 1provided by HGNC
    Primary source
    HGNC:HGNC:11231
    See related
    Ensembl:ENSG00000198513 MIM:606439; AllianceGenome:HGNC:11231
    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
    FSP1; GBP3; SPG3; HSN1D; SPG3A; AD-FSP; atlastin1
    Summary
    The protein encoded by this gene is a GTPase and a Golgi body transmembrane protein. The encoded protein can form a homotetramer and has been shown to interact with spastin and with mitogen-activated protein kinase kinase kinase kinase 4. This protein may be involved in axonal maintenance as evidenced by the fact that defects in this gene are a cause of spastic paraplegia type 3. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in brain (RPKM 34.8), endometrium (RPKM 5.1) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATL1 in Genome Data Viewer
    Location:
    14q22.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (50533082..50633068)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (44738771..44839213)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (50999800..51099786)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase kinase kinase 5 Neighboring gene zinc finger protein 678 pseudogene Neighboring gene uncharacterized LOC124903312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:51026957-51027456 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8360 Neighboring gene RNA, 7SL, cytoplasmic 452, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:51123951-51124450 Neighboring gene salvador family WW domain containing protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8361 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5725 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5726 Neighboring gene ZFP64 zinc finger protein pseudogene 1

    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. Targeted high-throughput sequencing identifies mutations in atlastin-1 as a cause of hereditary sensory neuropathy type I. Guelly C, et al. Am J Hum Genet, 2011 Jan 7. PMID 21194679, Free PMC Article
    2. A SPG3A mutation with a novel foot phenotype of hereditary spastic paraplegia in a Chinese Han family. Li XH, et al. Chin Med J (Engl), 2007 May 5. PMID 17531128
    3. Extending the clinical spectrum of SPG3A mutations to a very severe and very early complicated phenotype. Haberlová J, et al. J Neurol, 2008 Jun. PMID 18446315
    4. Four novel SPG3A/atlastin mutations identified in autosomal dominant hereditary spastic paraplegia kindreds with intra-familial variability in age of onset and complex phenotype. Smith BN, et al. Clin Genet, 2009 May. PMID 19459885
    5. Atlastin-1, the dynamin-like GTPase responsible for spastic paraplegia SPG3A, remodels lipid membranes and may form tubules and vesicles in the endoplasmic reticulum. Muriel MP, et al. J Neurochem, 2009 Sep. PMID 19573020

    See all (127) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Patients with complex and very-early-onset ATL1-related spastic paraplegia offer insights on genotype/phenotype correlations and support for autosomal recessive forms of SPG3A.
      Title: Patients with complex and very-early-onset ATL1-related spastic paraplegia offer insights on genotype/phenotype correlations and support for autosomal recessive forms of SPG3A.
    2. Atlastin-1 regulates endosomal tubulation and lysosomal proteolysis in human cortical neurons.
      Title: Atlastin-1 regulates endosomal tubulation and lysosomal proteolysis in human cortical neurons.
    3. Helical domain of hGBP3 cannot stimulate the second phosphate cleavage of GTP.
      Title: Helical domain of hGBP3 cannot stimulate the second phosphate cleavage of GTP.
    4. A novel homozygous variant in ATL1 associated with early onset spastic paraplegia 3A: Further evidence for autosomal recessive inheritance.
      Title: A novel homozygous variant in ATL1 associated with early onset spastic paraplegia 3A: Further evidence for autosomal recessive inheritance.
    5. Targeting of FSP1 regulates iron homeostasis in drug-tolerant persister head and neck cancer cells via lipid-metabolism-driven ferroptosis.
      Title: Targeting of FSP1 regulates iron homeostasis in drug-tolerant persister head and neck cancer cells via lipid-metabolism-driven ferroptosis.
    6. DNA methylation-regulated LINC02587 inhibits ferroptosis and promotes the progression of glioma cells through the CoQ-FSP1 pathway.
      Title: DNA methylation-regulated LINC02587 inhibits ferroptosis and promotes the progression of glioma cells through the CoQ-FSP1 pathway.
    7. FSP1 confers ferroptosis resistance in KEAP1 mutant non-small cell lung carcinoma in NRF2-dependent and -independent manner.
      Title: FSP1 confers ferroptosis resistance in KEAP1 mutant non-small cell lung carcinoma in NRF2-dependent and -independent manner.
    8. Copy number variations in SPAST and ATL1 are rare among Brazilians.
      Title: Copy number variations in SPAST and ATL1 are rare among Brazilians.
    9. Circ-ATL1 silencing reverses the activation effects of SIRT5 on smooth muscle cellular proliferation, migration and contractility in intracranial aneurysm by adsorbing miR-455.
      Title: Circ-ATL1 silencing reverses the activation effects of SIRT5 on smooth muscle cellular proliferation, migration and contractility in intracranial aneurysm by adsorbing miR-455.
    10. De novo variants cause complex symptoms in HSP-ATL1 (SPG3A) and uncover genotype-phenotype correlations.
      Title: De novo variants cause complex symptoms in HSP-ATL1 (SPG3A) and uncover genotype-phenotype correlations.
    Submit: New GeneRIF Correction See all GeneRIFs (78)

    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 3A
    MedGen: C2931355 OMIM: 182600 GeneReviews: Spastic Paraplegia 3A
    		not available
    Neuropathy, hereditary sensory, type 1D
    MedGen: C3150972 OMIM: 613708 GeneReviews: Spastic Paraplegia 3A
    		not available

    EBI GWAS Catalog

    Description
    Common genetic variation and performance on standardized cognitive tests.
    EBI GWAS Catalog
    Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years.
    EBI GWAS Catalog
    Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
    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

    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 GTP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTP binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axonogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in endoplasmic reticulum organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in endoplasmic reticulum tubular network membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein homooligomerization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein homooligomerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in Golgi cis cisterna ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum tubular network ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum tubular network membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    atlastin-1
    Names
    GBP-3
    GTP-binding protein 3
    brain-specific GTP-binding protein
    guanine nucleotide-binding protein 3
    guanylate-binding protein 3
    hGBP3
    spastic paraplegia 3 protein A
    NP_001121185.1
    NP_056999.2
    NP_853629.2
    XP_047287386.1
    XP_054232139.1
    XP_054232140.1
    XP_054232141.1

    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_009028.1 RefSeqGene

      Range
      5001..104987
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_360

    mRNA and Protein(s)

    1. NM_001127713.1 → NP_001121185.1  atlastin-1 isoform b

      See identical proteins and their annotated locations for NP_001121185.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and differs in the 5' UTR compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode isoform b.
      Source sequence(s)
      AK223436, AK290185, AL833591, DA397302, R61338
      Consensus CDS
      CCDS32077.1
      UniProtKB/TrEMBL
      A0A0S2Z5A2, Q53F53
      Related
      ENSP00000413675.2, ENST00000441560.6
      Conserved Domains (1) summary
      pfam02263
      Location:43 → 314
      GBP; Guanylate-binding protein, N-terminal domain

    2. NM_015915.5 → NP_056999.2  atlastin-1 isoform a

      See identical proteins and their annotated locations for NP_056999.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AK223436, AK290185, DA088230
      Consensus CDS
      CCDS9700.1
      UniProtKB/Swiss-Prot
      A6NND5, A8K2C0, G5E9T1, O95890, Q69YH7, Q8WXF7, Q96FK0
      UniProtKB/TrEMBL
      A0A0S2Z5B0, Q53F53
      Related
      ENSP00000351155.7, ENST00000358385.12
      Conserved Domains (1) summary
      pfam02263
      Location:43 → 314
      GBP; Guanylate-binding protein, N-terminal domain

    3. NM_181598.4 → NP_853629.2  atlastin-1 isoform b

      See identical proteins and their annotated locations for NP_853629.2

      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. Variants 2 and 3 both encode isoform b.
      Source sequence(s)
      AK223436, AK290185, AL833591, DA088230, R61338
      Consensus CDS
      CCDS32077.1
      UniProtKB/TrEMBL
      A0A0S2Z5A2, Q53F53
      Related
      ENSP00000519225.1, ENST00000713928.1
      Conserved Domains (1) summary
      pfam02263
      Location:43 → 314
      GBP; Guanylate-binding protein, N-terminal domain

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      50533082..50633068
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431430.1 → XP_047287386.1  atlastin-1 isoform X1

      UniProtKB/Swiss-Prot
      A6NND5, A8K2C0, G5E9T1, O95890, Q69YH7, Q8WXF7, Q96FK0
      UniProtKB/TrEMBL
      A0A0S2Z5B0

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      44738771..44839213
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376165.1 → XP_054232140.1  atlastin-1 isoform X1

      UniProtKB/Swiss-Prot
      A6NND5, A8K2C0, G5E9T1, O95890, Q69YH7, Q8WXF7, Q96FK0
      UniProtKB/TrEMBL
      A0A0S2Z5B0

    2. XM_054376166.1 → XP_054232141.1  atlastin-1 isoform X2

      UniProtKB/TrEMBL
      A0A0S2Z5A2

    3. XM_054376164.1 → XP_054232139.1  atlastin-1 isoform X1

      UniProtKB/Swiss-Prot
      A6NND5, A8K2C0, G5E9T1, O95890, Q69YH7, Q8WXF7, Q96FK0
      UniProtKB/TrEMBL
      A0A0S2Z5B0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WXF7.1 GenPept UniProtKB/Swiss-Prot:Q8WXF7

    Gene LinkOut

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

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