TKT p.Ile360=
c.1080C>T · rs908872216 · VCV3040262
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Conditions
1
TKT-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -5.5 |
| Overall | ||
| CADD | 2.616 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00202%
Overall
0.00285%
46/1,614,106 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Admixed American | 0.005% | 20,004 |
| African / African-American | 0.004% | 24,979 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
| European (non-Finnish) | 0.00314% | 31,893 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TKT
- Protein
- p.Ile360=
- Coding
- c.1080C>T
- MANE Select
- NM_001064
- dbSNP
- rs908872216
- Type
- single nucleotide variant
- Location
- chr3:53230484 (GRCh38)
- Gene constraint
- LOEUF 0.923 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.11 · 13 PDB
- Residue 360
- a β-strand
Disease context
TKT-related disorder
Similar variants
- TKT p.Glu94Lys Uncertain significance ⚠ same condition
- TKT p.Ala213= Likely benign same condition
- TKT p.Leu51= Likely benign same condition
- TKT p.Pro192= Likely benign same condition
- TKT p.Ser406= Likely benign same condition
- TKT p.Arg591Trp Uncertain significance ★★ ⚠ same type
- TKT p.Asp106Tyr Uncertain significance ★★ ⚠ same type
- TKT p.Leu153Pro Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tkt-p-ile360 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown