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ATL1 atlastin GTPase 1 [ Homo sapiens (human) ]

Gene ID: 51062, updated on 20-Apr-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
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Genomic context

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Location:
14q22.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (50533082..50633068)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (44738771..44839213)
105.20220307 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
  • 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. De novo variants cause complex symptoms in HSP-ATL1 (SPG3A) and uncover genotype-phenotype correlations. Alecu JE, et al. Hum Mol Genet, 2023 Jan 1. PMID 35925862, Free PMC Article
  2. Reduced penetrance of an eastern French mutation in ATL1 autosomal-dominant inheritance (SPG3A): extended phenotypic spectrum coupled with brain (18)F-FDG PET. Hocquel A, et al. Neurogenetics, 2022 Oct. PMID 35788923
  3. A novel insertion mutation in atlastin 1 is associated with spastic quadriplegia, increased membrane tethering, and aberrant conformational switching. Kelly CM, et al. J Biol Chem, 2022 Jan. PMID 34808209, Free PMC Article
  4. The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation. Kelly CM, et al. J Cell Biol, 2021 Nov 1. PMID 34546351, Free PMC Article
  5. Clinical and genetic characterization of hereditary spastic paraplegia type 3A in Taiwan. Hsu SL, et al. Parkinsonism Relat Disord, 2021 Jun. PMID 34015694

See all (117) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Copy number variations in SPAST and ATL1 are rare among Brazilians.
    Title: Copy number variations in SPAST and ATL1 are rare among Brazilians.
  7. 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.
  8. 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.
  9. Reduced penetrance of an eastern French mutation in ATL1 autosomal-dominant inheritance (SPG3A): extended phenotypic spectrum coupled with brain (18)F-FDG PET.
    Title: Reduced penetrance of an eastern French mutation in ATL1 autosomal-dominant inheritance (SPG3A): extended phenotypic spectrum coupled with brain (18)F-FDG PET.
  10. A novel insertion mutation in atlastin 1 is associated with spastic quadriplegia, increased membrane tethering, and aberrant conformational switching.
    Title: A novel insertion mutation in atlastin 1 is associated with spastic quadriplegia, increased membrane tethering, and aberrant conformational switching.
Submit: New GeneRIF Correction See all GeneRIFs (76)

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
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
    ENSP00000450989.2, ENST00000553509.2
    Conserved Domains (1) summary
    pfam02263
    Location:43 → 314
    GBP; Guanylate-binding protein, N-terminal domain

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_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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