TDO2 p.Ser402=
c.1206T>C · rs763263639 · VCV3039864
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Conditions
1
TDO2-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 -0.57 | GERP -1.2, phastCons 0.07 |
| Overall | ||
| CADD | 5.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,734 alleles
Filtering AF
0.00546%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00382%
Overall
0.00118%
19/1,612,796 alleles · ultra-rare
exomes 16/1,460,592 · genomes 3/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,533 |
| African / African-American | 0.0107% | 9,358 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,607 |
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
- TDO2
- Protein
- p.Ser402=
- Coding
- c.1206T>C
- MANE Select
- NM_005651
- dbSNP
- rs763263639
- Type
- single nucleotide variant
- Location
- chr4:155919975 (GRCh38)
- Gene constraint
- LOEUF 1.104 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.63 · 22 PDB
Disease context
TDO2-related disorder
Similar variants
- TDO2 p.Asn229His Benign same condition
- TDO2 p.Leu226= Likely benign same condition
- TDO2 p.Phe268Tyr Likely benign same condition
- TPH2 p.Pro206Ser Uncertain significance ★★ ⚠ same type
- TDO2 p.Val306= Benign/Likely benign ★★ same type
- TPH2 c.-52A>G Benign ★★ same type
- TPH2 c.*149G>A Likely benign ★★ same type
- TPH2 c.*479G>A 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/tdo2-p-ser402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown