Gene
TSC1
TSC complex subunit 1
- HGNC 12362(opens in a new tab)
- Ensembl gene ENSG00000165699(opens in a new tab)
- NCBI Gene 7248(opens in a new tab)
Summary
- Cytogenetic location
- 9q34.13
- Coordinates
- Chromosome 9: 132,891,349–132,944,616 (GRCh38)
- Exons
- 23 exons across 53.3 kb
- Protein
- 1,164 amino acids
- Inheritance
- Autosomal dominant
- Also known as
- KIAA0243, LAM, hamartin
- Previous symbols
- TSC
- MANE Select transcript
- ENST00000298552.9NM_000368.5
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Tuberous Sclerosis
- Autosomal dominant
Hereditary disease characterized by seizures, intellectual disability, developmental delay, and skin and ocular lesions. First signs usually occur during infancy or childhood but in rare cases may not occur until 2nd or 3rd decade.
- 4 GenCC submitters rate it definitive or strong
- On the ACMG secondary findings list
What knowing changes
mTOR inhibitors, antiepileptic drugs, surveillance imaging, surgical management of complications
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 TSC1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
- Variants with a page
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 8.6 kb of the gene's 53.3 kb; 3,495 of those bases code for the protein.
How a genome test reads TSC1
564
positions in TSC1 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 53.3 kb of TSC1, introns included, not only the 8.6 kb of exons.
Variants with a page (115)
The TSC1 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | HGVS c. | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|---|
| A283Pfs*35 | c.846del | Exon 9 | 132,912,348 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| c.107-1G>A | Intron 3 | 132,927,305 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.211-1G>A | Intron 4 | 132,925,740 | Pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.211-2A>C | Intron 4 | 132,925,741 | Pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.363+1G>T | Intron 5 | 132,925,586 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.363+668G>T | Intron 5 | 132,924,919 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.364-2A>G | Intron 5 | 132,923,494 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.508+2T>C | Intron 6 | 132,923,346 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.509-1G>A | Intron 6 | 132,921,974 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.663+1G>A | Intron 7 | 132,921,818 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts |
Traits linked to TSC1
The Human Phenotype Ontology lists these as features of the rare conditions TSC1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Autism spectrum disorder
- Behavioral abnormality
- Cortical dysplasia
- Cortical tubers
- Epilepsy
- Subependymal nodules
- Abnormal social behavior
- Aggressive behavior
Show 30 more traits
- Autism
- Depression
- Difficulty sleeping
- Epileptic spasm
- Impulsivity
- Infantile spasms
- Intellectual disability
- More active than typical
- Neurodevelopmental delay
- Repeated seizures without recovery between them
- Repetitive compulsive behavior
- Seizure affecting one half of brain
- Self-injurious behavior
- Specific learning disability
- Anxiety
- Attention deficit
- Cognitive impairment
- Noncommunicating hydrocephalus
- Poor speech
- Subependymal giant-cell astrocytoma
- Too much cerebrospinal fluid in the brain
- Astrocytoma
- Astrocytosis
- Ependymoma
- Focal cortical dysplasia type II
- Focal impaired awareness seizure
- Focal white matter lesions
- Hemimegalencephaly
- Optic nerve glioma
- Weakness of one side of body
Abnormality of the respiratory system
- Breathing difficulty
- Cough
- Lung infiltrates
- Stiff lung or chest wall causing decreased lung volume
- Collapsed lung
- Emphysema
- Partial or complete collapse of part or entire lung
- Breathing difficulties
Show 3 more traits
External links
Gene records
Transcript
Protein
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
Dante Labs. (n.d.). TSC1 gene: TSC complex subunit 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/tsc1
Dante Labs. TSC1 gene: TSC complex subunit 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/tsc1
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