AtlasGene
SPTAN1
spectrin alpha, non-erythrocytic 1
- HGNC 11273↗(opens in a new tab)
- Ensembl gene ENSG00000197694↗(opens in a new tab)
- NCBI Gene 6709↗(opens in a new tab)
Summary
- Cytogenetic location
- 9q34.11
- Coordinates
- Chromosome 9: 128,552,587–128,633,662 (GRCh38)
- Exons
- 57 exons across 81.1 kb
- Protein
- 2,477 amino acids
- MANE Select transcript
- ENST00000372739.7NM_001130438.3
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
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Get my Genome TestCurated reports relevant to this gene
Charcot-Marie-Tooth Disease
- Distal Hereditary Motor Neuropathy
Inherited neuropathies that mainly affect motor nerves, causing weakness and wasting of the hands and feet, including SORD-related neuropathy.
- 1 GenCC submitter rates it definitive or strong
Spinal Muscular Atrophy
A group of disorders characterised by degeneration of spinal cord anterior horn cells, leading to progressive muscle weakness and atrophy.
- 1 GenCC submitter rates it definitive or strong
▶Actionability
Gene therapy (onasemnogene abeparvovec), antisense oligonucleotide therapy (nusinersen), oral splicing modifier (risdiplam), supportive care
Broader groupings
Epilepsy (Full Panel)
- Epilepsy
One of 171 genes linked to it
A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.
- ClinGen rates the link definitive
- 6 GenCC submitters rate it definitive or strong
Hereditary Spastic Paraplegia
- 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.
- 1 GenCC submitter rates it definitive or strong
How SPTAN1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
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 7.9 kb of the gene's 81.1 kb; 7,434 of those bases code for the protein.
Sequencing SPTAN1
0Low
How hard SPTAN1 is to sequence with short reads, out of 100Each bar is the share of SPTAN1's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.0%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.3.3%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
62
positions in SPTAN1 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 81.1 kb of SPTAN1, introns included, not only the 7.9 kb of exons.
Genes linked to the same conditions
- BSCL2BSCL2 lipid droplet biogenesis associated, seipinShares 3 conditions
- REEP1receptor accessory protein 1Shares 3 conditions
- ATP7AATPase copper transporting alphaShares 2 conditions
- DCTN1dynactin subunit 1Shares 2 conditions
- DNAJB2DnaJ heat shock protein family (Hsp40) member B2Shares 2 conditions
- DYNC1H1dynein cytoplasmic 1 heavy chain 1Shares 2 conditions
- EMILIN1elastin microfibril interfacer 1Shares 2 conditions
- FBXO38F-box protein 38Shares 2 conditions
- GARS1glycyl-tRNA synthetase 1Shares 2 conditions
- HACE1HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1Shares 2 conditions
- HSPB8heat shock protein family B (small) member 8Shares 2 conditions
- IGHMBP2immunoglobulin mu DNA binding protein 2Shares 2 conditions
Traits linked to SPTAN1
The Human Phenotype Ontology lists these as features of the rare conditions SPTAN1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Abnormal gait
- Babinski sign
- Brisk knee jerk
- Clumsiness
- Decreased compound muscle action potential amplitude
- Delayed speech and language development
- Epilepsy
- High stepping
Show 46 more traits
- Impaired vibratory sensation
- IQ less than 20
- Jerking
- Loss of ability to walk
- Motor axonal neuropathy
- Motor delay
- Numbness
- Paroxysmal dyskinesia
- Peripheral axonal neuropathy
- Peripheral neuropathy
- Reading disability
- Reduced cerebral white matter volume
- Seizure affecting one half of brain
- Unsteady walk
- Wide based walk
- Willis-Ekbom disease
- Abnormal pyramidal sign
- Hypsarrhythmia
- Infantile spasms
- Loss of developmental milestones
- Abnormality of the nervous system
- Ataxia
- Atrophy/Degeneration affecting the brainstem
- Autism spectrum disorder
- Decrease in size of the outer layer of the brain due to loss of brain cells
- Degeneration of cerebellum
- Intellectual disability
- Underdevelopment of part of brain called corpus callosum
- Attention deficit
- Brief seizures with staring spells
- Dystonia
- EEG with frontal focal spikes
- EEG with polyspike wave complexes
- Febrile seizure (within the age range of 3 months to 6 years)
- Multifocal epileptiform discharges
- Myoclonic seizure
- Difficulty articulating speech
- Focal impaired awareness seizure
- Grand mal seizures
- Overactive lower leg reflex
- Sudden loss of muscle tone
- CNS hypomyelination
- Degeneration of cerebrum
- Epileptic encephalopathy
- Increased reflexes
- Intellectual disability, severe
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 Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- 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.). SPTAN1 gene: spectrin alpha, non-erythrocytic 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/sptan1
Dante Labs. SPTAN1 gene: spectrin alpha, non-erythrocytic 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/sptan1
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