AtlasGene
TKT
transketolase
- HGNC 11834↗(opens in a new tab)
- Ensembl gene ENSG00000163931↗(opens in a new tab)
- NCBI Gene 7086↗(opens in a new tab)
Summary
- Cytogenetic location
- 3p21.1
- Coordinates
- Chromosome 3: 53,224,712–53,256,022 (GRCh38)
- Exons
- 14 exons across 31.3 kb
- Protein
- 623 amino acids
- MANE Select transcript
- ENST00000462138.6NM_001064.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/tkt.json"
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No Genome Test report reads TKT yet. The test sequences your whole genome, so your data includes it all the same.
How TKT 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 3 kb of the gene's 31.3 kb; 1,872 of those bases code for the protein.
Sequencing TKT
2Easy
How hard TKT is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of TKT's exons sit where short reads map cleanly.
What adds to it: the share of TKT'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 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%.0.9%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.15%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
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 TKT'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.
3
positions in TKT 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 31.3 kb of TKT, introns included, not only the 3 kb of exons.
ClinVar pathogenic variants (3)
The TKT 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.
- Likely pathogenic 3
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_001064.4(TKT):c.1697-1G>A (opens in a new tab) | transketolase deficiency | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001135055.2:c.769_770insCTACCTCCTTATCTTCTG (opens in a new tab) | transketolase deficiency | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_001064.4(TKT):c.181C>T (p.Gln61Ter) (opens in a new tab) | transketolase deficiency | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Traits linked to TKT
The Human Phenotype Ontology lists these as features of the rare conditions TKT can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Delayed speech and language development
- Global developmental delay
- Absent speech development
- Attention deficit
- Intellectual disability
- Intellectual disability, mild
- Obsessive compulsive behavior
- Repetitive movements
Show 1 more trait
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.
- 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 2026.10.18-8b139e39.
Cite this page
Dante Labs. (n.d.). TKT gene: transketolase. Retrieved 18 October 2026, from https://dantelabs.com/genes/tkt
Dante Labs. TKT gene: transketolase [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/tkt
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