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Gene

ATL1

atlastin GTPase 1

Summary

Cytogenetic location
14q22.1
Coordinates
Chromosome 14: 50,560,145–50,633,045 (GRCh38)
Exons
14 exons across 72.9 kb
Protein
558 amino acids
Inheritance
Autosomal dominant
Also known as
FSP1, AD-FSP
Previous symbols
SPG3, SPG3A
MANE Select transcript
ENST00000358385.12NM_015915.5
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Hereditary Sensory and Autonomic Neuropathies (incl. Familial Dysautonomia)

    • Hereditary Sensory and Autonomic Neuropathy

      A group of neuropathies, including familial dysautonomia (ELP1), HSAN1 (SPTLC1/SPTLC2), HSAN2 (WNK1, RETREG1) and congenital insensitivity to pain (NTRK1, SCN9A, PRDM12), most of which are recessive while HSAN1 is dominant.

      • ClinGen rates the link definitive
      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Protection against unnoticed injuries, burns and infections, management of autonomic symptoms, and carrier testing for relatives (familial dysautonomia is included in Ashkenazi Jewish carrier screening).

  • Hereditary Spastic Paraplegia

    • Hereditary Spastic Paraplegia 3aAutosomal dominant

      Any hereditary spastic paraplegia in which the cause of the disease is a mutation in the ATL1 gene.

      • 4 GenCC submitters rate it definitive or strong
    • Hereditary Spastic Paraplegia (All Types)

      One of 66 genes linked to it

      Umbrella term covering all hereditary spastic paraplegias, including SPG4 (SPAST), the most common dominant form, and SPG5A, SPG6, SPG10, SPG18, SPG30 and SPG31.

      • 4 GenCC submitters rate it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How ATL1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 14, with a bracket where ATL1 sits. ATL1 and 11 genes near it on chromosome 14, from 50,096,595 to 51,096,594.Chromosome 1414q22.1p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.11q32.12q32.13q32.2q32.31q32.32q32.3350.2 Mb50.4 Mb50.6 Mb50.8 Mb51 MbVCPKMT: 50,108,631–50,116,600, reverse strandVCPKMTSOS2: 50,116,801–50,231,930, reverse strandSOS2L2HGDH: 50,237,563–50,312,243, reverse strandL2HGDHDMAC2L: 50,311,516–50,356,756, forward strandDMAC2LCDKL1: 50,326,265–50,416,461, reverse strandCDKL1MAP4K5: 50,417,845–50,561,126, reverse strandMAP4K5ATL1: 50,560,145–50,633,045, forward strandATL1SAV1: 50,626,616–50,668,600, reverse strandSAV1NIN: 50,719,763–50,832,038, reverse strandNINPYGL: 50,857,891–50,944,734, reverse strandPYGLABHD12B: 50,872,046–50,904,970, forward strandABHD12BTRIM9: 50,975,254–51,096,084, reverse strandTRIM9Diagram of ATL1: 14 exons on the forward strand of chromosome 14Exon 2: 2 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 4: 9 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 6: 5 known disease-causing sitesExon 7: 4 known disease-causing sitesExon 8: 6 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 10: 8 known disease-causing sitesExon 11: 8 known disease-causing sitesExon 12: 27 known disease-causing sitesExon 1: 50,560,145–50,560,299, 155 basesExon 2: 50,587,831–50,588,078, 248 basesExon 3: 50,590,941–50,591,075, 135 basesExon 4: 50,591,535–50,591,639, 105 basesExon 5: 50,593,846–50,593,896, 51 basesExon 6: 50,595,576–50,595,632, 57 basesExon 7: 50,613,259–50,613,351, 93 basesExon 8: 50,614,373–50,614,511, 139 basesExon 9: 50,620,599–50,620,726, 128 basesExon 10: 50,621,843–50,621,899, 57 basesExon 11: 50,623,177–50,623,248, 72 basesExon 12: 50,628,031–50,628,462, 432 basesExon 13: 50,629,995–50,630,009, 15 basesExon 14: 50,632,229–50,633,045, 817 bases124681012145′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.5 kb of the gene's 72.9 kb; 1,677 of those bases code for the protein.

How a genome test reads ATL1

77

positions in ATL1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 72.9 kb of ATL1, introns included, not only the 2.5 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). ATL1 gene: atlastin GTPase 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/atl1

Vancouver

Dante Labs. ATL1 gene: atlastin GTPase 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atl1

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