AtlasGene
SPART
spartin
- HGNC 18514↗(opens in a new tab)
- Ensembl gene ENSG00000133104↗(opens in a new tab)
- NCBI Gene 23111↗(opens in a new tab)
Summary
- Cytogenetic location
- 13q13.3
- Coordinates
- Chromosome 13: 36,301,638–36,346,394 (GRCh38)
- Exons
- 9 exons across 44.8 kb
- Protein
- 666 amino acids
- Also known as
- KIAA0610, TAHCCP1
- Previous symbols
- SPG20
- MANE Select transcript
- ENST00000438666.7NM_015087.5
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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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.
- ClinGen rates the link definitive
- 1 GenCC submitter rates it definitive or strong
Inherited Neurodegenerative Disorders
- KIF5A-Related Neurodegenerative DisorderAutosomal dominant
One of 372 genes linked to it
Caused by changes in one copy of KIF5A, which encodes a motor protein with a cargo-binding tail. Different types of change lead to different conditions: hereditary spastic paraplegia type 10, an axonal form of Charcot-Marie-Tooth disease and amyotrophic lateral sclerosis (ALS).
- ClinGen rates the link definitive
- 1 GenCC submitter rates it definitive or strong
▶Actionability
Care is symptomatic and depends on the presentation, including physiotherapy, antispasticity medicines and multidisciplinary ALS care. Each child of an affected person has a 1 in 2 chance of inheriting the change; genetic counselling helps families understand this.
How SPART 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 4.9 kb of the gene's 44.8 kb; 2,001 of those bases code for the protein.
Sequencing SPART
3Easy
How hard SPART is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of SPART's exons sit where short reads map cleanly.
What adds to it: the share of SPART's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 100%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 60%.0%
- Shared with chrYThe pseudoautosomal regions and the X-transposed region, where chrX and chrY carry the same or nearly the same sequence, so reads from either may land on the other. Weight 60%.0%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 50%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 30%.3.7%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 20%.9.5%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of SPART's exon bases in that kind of difficult region. Any one kind can make a gene hard on its own, and each further kind adds less: 0 when no base is in any, 100 when every base is where reads cannot be placed uniquely.
14
positions in SPART 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 44.8 kb of SPART, introns included, not only the 4.9 kb of exons.
ClinVar pathogenic variants (14)
The SPART variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 7
- Likely pathogenic 7
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_015087.5(SPART):c.364_365del (p.Met122fs) (opens in a new tab) | Troyer syndrome | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_015087.5(SPART):c.1474_1477del (p.Gln492fs) (opens in a new tab) | Troyer syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.1450dup (p.Thr484fs) (opens in a new tab) | Troyer syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.1369C>T (p.Arg457Ter) (opens in a new tab) | Troyer syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.1294del (p.Ser432fs) (opens in a new tab) | Troyer syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.1110del (p.Lys370fs) (opens in a new tab) | Troyer syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.894_898del (p.Met299fs) (opens in a new tab) | Troyer syndrome | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.1738G>T (p.Gly580Ter) (opens in a new tab) | Troyer syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.1440_1444dup (p.Gln482fs) (opens in a new tab) | Troyer syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.1324G>C (p.Ala442Pro) (opens in a new tab) | Troyer syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.745C>T (p.Arg249Ter) (opens in a new tab) | Troyer syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.696dup (p.Val233fs) (opens in a new tab) | Troyer syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.685C>T (p.Gln229Ter) (opens in a new tab) | Troyer syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_015087.5(SPART):c.592G>T (p.Gly198Ter) (opens in a new tab) | Troyer syndrome | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Genes linked to the same conditions
- ABCD1ATP binding cassette subfamily D member 1Shares 2 conditions
- ABHD16Aabhydrolase domain containing 16A, phospholipaseShares 2 conditions
- ALDH18A1aldehyde dehydrogenase 18 family member A1Shares 2 conditions
- AMFRautocrine motility factor receptorShares 2 conditions
- AP4B1adaptor related protein complex 4 subunit beta 1Shares 2 conditions
- AP4E1adaptor related protein complex 4 subunit epsilon 1Shares 2 conditions
- AP4M1adaptor related protein complex 4 subunit mu 1Shares 2 conditions
- AP4S1adaptor related protein complex 4 subunit sigma 1Shares 2 conditions
- AP5Z1adaptor related protein complex 5 subunit zeta 1Shares 2 conditions
- ARL6IP1ARL6 interacting reticulophagy regulator 1Shares 2 conditions
- ATL1atlastin GTPase 1Shares 2 conditions
- ATP13A2ATPase cation transporting 13A2Shares 2 conditions
Traits linked to SPART
The Human Phenotype Ontology lists these as features of the rare conditions SPART can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Babinski sign
- Difficulty articulating speech
- Impaired vibration sensation at ankles
- Increased reflexes
- Intellectual disability, mild
- Lack of coordination of movement
- Motor delay
- Abnormal shape of brain
Show 17 more traits
- Abnormality of the cerebellum
- Cognitive impairment
- Delayed speech and language development
- Global developmental delay
- Impaired vibratory sensation
- Slurred speech
- Specific learning disability
- Anxiety
- Can't control feelings
- Difficulty sleeping
- Hallucinations
- Panic attack
- Psychosis
- Speech apraxia
- Abnormal gait
- Degeneration of cerebellum
- Knee clonus
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 2026-10-19: 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 2026.10.19-9814e911.
Cite this page
Dante Labs. (n.d.). SPART gene: spartin. Retrieved 19 October 2026, from https://dantelabs.com/genes/spart
Dante Labs. SPART gene: spartin [Internet]. [cited 19 October 2026]. Available from: https://dantelabs.com/genes/spart
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