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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
ATL1
atlastin GTPase 1
Chromosome 14 Β· 14q22.1
NCBI Gene: 51062Ensembl: ENSG00000198513.16HGNC: HGNC:11231UniProt: A0A0S2Z5A2
131PubMed Papers
22Diseases
0Drugs
92Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
endoplasmic reticulum membrane fusionGTPase-dependent fusogenic activityendoplasmic reticulum tubular network membrane organizationendoplasmic reticulum tubular network membranehereditary spastic paraplegia 3AAutosomal dominant spastic paraplegia type 3hereditary sensory and autonomic neuropathy type 1hereditary spastic paraplegia
✦AI Summary

ATL1 (atlastin GTPase 1) is a membrane-anchored GTPase that mediates GTP-dependent fusion of endoplasmic reticulum (ER) membranes, maintaining the continuous ER network architecture 1. ATL1 facilitates formation of three-way junctions where ER tubules intersect through a conserved molecular mechanism: two ATL1 molecules on neighboring ER tubules bind GTP and form homodimers via their G domains and 3HB regions 1. Upon GTP hydrolysis, the 3HB regions tighten, pulling membranes together to drive fusion; subsequent GDP release resets monomers for new fusion cycles 1. Beyond ER morphology, ATL1 regulates endosomal tubulation and lysosomal proteolysis in human neurons 2. ATL1 mutations represent a significant cause of hereditary spastic paraplegia (HSP-ATL1/SPG3A), with ATL1 mutations identified in >1% of HSP cases in large cohorts 3. De novo ATL1 variants cause early, complex symptoms extending beyond typical pure HSP, including neurodevelopmental abnormalities, upper limb spasticity, bulbar symptoms, and brain imaging abnormalities 4. ATL1 deficiency in human cortical neurons results in altered ER morphology with reduced three-way junctions, defective endosomal tubule dynamics, and impaired lysosomal function 2, linking ER morphology dysfunction to broader cellular proteolytic deficits in neurodegeneration.

Sources cited
1
ATL1 is a membrane regulator of ER formation and works with VCP to regulate ER morphology and protein synthesis efficiency; ATL1 mutations cause HSP and are involved in neurological disorders
PMID: 29310658
2
ATL1 mutations represent >1% of hereditary spastic paraplegia cases in a large cohort of 1550 index patients
PMID: 34983064
3
De novo ATL1 variants cause early, complex HSP phenotypes with neurodevelopmental abnormalities, upper limb spasticity, bulbar symptoms, and peripheral neuropathy; genotype-phenotype correlations exist based on variant localization
PMID: 35925862
4
ATL1 is required for correct ER morphology in human cortical neurons; ATL1 deficiency causes reduced three-way junctions, impaired endosomal tubulation, and reduced lysosomal proteolytic capacity
PMID: 38851544
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜22
hereditary spastic paraplegia 3AOpen Targets
0.83Strong
Autosomal dominant spastic paraplegia type 3Open Targets
0.80Strong
hereditary sensory and autonomic neuropathy type 1Open Targets
0.65Moderate
hereditary spastic paraplegiaOpen Targets
0.65Moderate
Dupuytren ContractureOpen Targets
0.42Moderate
Spastic paraplegiaOpen Targets
0.40Moderate
genetic disorderOpen Targets
0.40Moderate
hereditary sensory and autonomic neuropathyOpen Targets
0.37Weak
Distal lower limb muscle weaknessOpen Targets
0.34Weak
Distal sensory impairmentOpen Targets
0.34Weak
Osteomyelitis leading to amputation due to slow healing fracturesOpen Targets
0.34Weak
Penetrating foot ulcersOpen Targets
0.34Weak
Neurodevelopmental delayOpen Targets
0.33Weak
arthritisOpen Targets
0.30Weak
Abnormal pyramidal signOpen Targets
0.27Weak
Abnormality of the nervous systemOpen Targets
0.27Weak
Abnormality of the skeletal systemOpen Targets
0.17Weak
Charcot-Marie-Tooth diseaseOpen Targets
0.14Weak
autosomal dominant complex spastic paraplegiaOpen Targets
0.12Weak
neoplasmOpen Targets
0.11Weak
Neuropathy, hereditary sensory, 1DUniProt
Spastic paraplegia 3, autosomal dominantUniProt
Pathogenic Variants92
NM_015915.5(ATL1):c.757G>A (p.Val253Ile)Pathogenic
Hereditary spastic paraplegia 3A|not provided|Hereditary spastic paraplegia
β˜…β˜…β˜†β˜†2025β†’ Residue 253
NM_015915.5(ATL1):c.715C>T (p.Arg239Cys)Pathogenic
Hereditary spastic paraplegia 3A|not provided|Hereditary spastic paraplegia 3A;Neuropathy, hereditary sensory, type 1D|Spastic paraplegia|Hereditary spastic paraplegia
β˜…β˜…β˜†β˜†2025β†’ Residue 239
NM_015915.5(ATL1):c.1483C>T (p.Arg495Trp)Pathogenic
Hereditary spastic paraplegia 3A|not provided|Inborn genetic diseases|Hereditary spastic paraplegia
β˜…β˜…β˜†β˜†2025β†’ Residue 495
NM_015915.5(ATL1):c.716G>A (p.Arg239His)Likely pathogenic
Hereditary spastic paraplegia 3A|Spastic paraplegia
β˜…β˜…β˜†β˜†2025β†’ Residue 239
NM_015915.5(ATL1):c.650G>A (p.Arg217Gln)Pathogenic
Hereditary spastic paraplegia 3A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 217
NM_015915.5(ATL1):c.773A>G (p.His258Arg)Pathogenic
Hereditary spastic paraplegia 3A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 258
NM_015915.5(ATL1):c.1243C>T (p.Arg415Trp)Pathogenic
Hereditary spastic paraplegia 3A|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 415
NM_015915.5(ATL1):c.1041G>A (p.Met347Ile)Pathogenic
Hereditary spastic paraplegia 3A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 347
NM_015915.5(ATL1):c.574C>T (p.Leu192Phe)Likely pathogenic
Hereditary spastic paraplegia 3A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 192
NM_015915.5(ATL1):c.1204T>C (p.Phe402Leu)Pathogenic
not provided|Hereditary spastic paraplegia 3A
β˜…β˜…β˜†β˜†2025β†’ Residue 402
NM_015915.5(ATL1):c.1208G>C (p.Arg403Pro)Likely pathogenic
Hereditary spastic paraplegia 3A
β˜…β˜…β˜†β˜†2025β†’ Residue 403
NM_015915.5(ATL1):c.1217AGA[1] (p.Lys407del)Pathogenic
Hereditary spastic paraplegia 3A|Hereditary spastic paraplegia|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 407
NM_015915.5(ATL1):c.467C>T (p.Thr156Ile)Pathogenic
Hereditary spastic paraplegia 3A|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 156
NM_015915.5(ATL1):c.1501C>T (p.Arg501Ter)Pathogenic
not provided|ATL1-related spastic paraplegia, recessive
β˜…β˜…β˜†β˜†2023β†’ Residue 501
NM_015915.5(ATL1):c.1223T>C (p.Met408Thr)Pathogenic
Hereditary spastic paraplegia 3A|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 408
NM_015915.5(ATL1):c.1220A>T (p.Lys407Met)Pathogenic
Inborn genetic diseases|Hereditary spastic paraplegia 3A
β˜…β˜…β˜†β˜†2023β†’ Residue 407
NM_015915.5(ATL1):c.466A>C (p.Thr156Pro)Pathogenic
Hereditary spastic paraplegia 3A
β˜…β˜…β˜†β˜†2023β†’ Residue 156
NM_015915.5(ATL1):c.1225G>T (p.Gly409Cys)Pathogenic
not provided|Hereditary spastic paraplegia 3A
β˜…β˜…β˜†β˜†2022β†’ Residue 409
NM_015915.5(ATL1):c.1228G>A (p.Gly410Arg)Pathogenic
not provided|Hereditary spastic paraplegia 3A
β˜…β˜…β˜†β˜†2022β†’ Residue 410
NM_015915.5(ATL1):c.1306_1308del (p.Asn436del)Pathogenic
Hereditary spastic paraplegia 3A|Hereditary spastic paraplegia
β˜…β˜…β˜†β˜†2020β†’ Residue 436
View on ClinVar β†—
Related Genes
ZFYVE27Protein interaction88%NIPA1Protein interaction87%RTN1Protein interaction85%RTN2Protein interaction85%REEP5Protein interaction85%RTN3Protein interaction83%
Tissue Expression6 tissues
Brain
100%
Ovary
12%
Bone Marrow
7%
Heart
5%
Lung
4%
Liver
1%
Gene Interaction Network
Click a node to explore
ATL1ZFYVE27NIPA1RTN1RTN2REEP5RTN3
PROTEIN STRUCTURE
Preparing viewer…
PDB6B9F Β· 1.90 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.57Moderately Constrained
pLIβ“˜
0.36Tolerant
Observed/Expected LoF0.41 [0.29–0.57]
RankingsWhere ATL1 stands among ~20K protein-coding genes
  • #3,547of 20,598
    Most Researched131 Β· top quartile
  • #833of 5,498
    Most Pathogenic Variants92 Β· top quartile
  • #3,746of 17,882
    Most Constrained (LOEUF)0.57 Β· top quartile
Genes detectedATL1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Clinical and genetic spectra of 1550 index patients with hereditary spastic paraplegia.
PMID: 34983064
Brain Β· 2022
1.00
2
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
0.90
3
The involvement of endoplasmic reticulum formation and protein synthesis efficiency in VCP- and ATL1-related neurological disorders.
PMID: 29310658
J Biomed Sci Β· 2018
0.80
4
Alkyltransferase-like proteins.
PMID: 17500045
DNA Repair (Amst) Β· 2007
0.70
5
The membrane curvature-inducing REEP1-4 proteins generate an ER-derived vesicular compartment.
PMID: 39368994
Nat Commun Β· 2024
0.60