TKT p.Ser43=
c.129C>T · rs201142076 · VCV748013
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.16%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.34 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | GERP -5.3 |
| Overall | ||
| CADD | 7.048 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.16%
East Asian · 72/44,884 alleles
Filtering AF
0.131%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.12%
Overall
0.00533%
86/1,614,056 alleles · rare
exomes 80/1,461,748 · genomes 6/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.16% | 623 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,803 |
| African / African-American | 0.004% | 25,013 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
| European (non-Finnish) | 0.000593% | 168,573 |
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.Ser43=
- Coding
- c.129C>T
- MANE Select
- NM_001064
- dbSNP
- rs201142076
- Type
- single nucleotide variant
- Location
- chr3:53242221 (GRCh38)
- Gene constraint
- LOEUF 0.923 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.11 · 13 PDB
Similar variants
- TKT p.Arg591Trp Uncertain significance ★★ ⚠ same type
- TKT p.Asp106Tyr Uncertain significance ★★ ⚠ same type
- TKT p.Leu153Pro Uncertain significance ★★ ⚠ same type
- TKT p.Leu98Pro Uncertain significance ★★ ⚠ same type
- TKT p.Tyr202Cys Uncertain significance ★★ same type
- TKT c.1264+17T>C Benign ★★ same type
- TKT c.1265-47G>C Benign ★★ same type
- TKT c.1697-49C>T Benign ★★ 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-ser43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown