TKT p.Pro192=
c.576G>A · rs201348801 · VCV3035207
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 -5 | GERP -5 |
| Overall | ||
| CADD | 3.448 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,014 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00322%
52/1,613,920 alleles · very rare
exomes 47/1,461,614 · genomes 5/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,002 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,833 |
| European (non-Finnish) | 0.00339% | 29,500 |
| South Asian | 0.0022% | 45,538 |
| Finnishnot grpmax-eligible | 0.00157% | 63,848 |
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.Pro192=
- Coding
- c.576G>A
- MANE Select
- NM_001064
- dbSNP
- rs201348801
- Type
- single nucleotide variant
- Location
- chr3:53235036 (GRCh38)
- Gene constraint
- LOEUF 0.923 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.11 · 13 PDB
- Residue 192
- a β-strand
Disease context
TKT-related disorder
Similar variants
- TKT p.Pro192Leu Uncertain significance ★ ⚠ same residue
- TKT p.Glu94Lys Uncertain significance ⚠ same condition
- TKT p.Ala213= Likely benign same condition
- TKT p.Ile360= Likely benign same condition
- TKT p.Leu51= 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
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-pro192 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown