TXN2 p.Ala87=
c.261A>C · rs749412225 · VCV2583003
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0177%, mid)
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 -0.9 | GERP -3.8, phastCons 0.012 |
| Overall | ||
| CADD | 12.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0177%
Middle Eastern · 1/5,646 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00236%
Overall
0.00366%
59/1,613,046 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0177% | 5,646 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,241 |
| Admixed American | 0.00834% | 11,997 |
| European (non-Finnish) | 0.00356% | 28,087 |
| African / African-American | 0.00133% | 74,938 |
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
- TXN2
- Protein
- p.Ala87=
- Coding
- c.261A>C
- MANE Select
- NM_012473
- dbSNP
- rs749412225
- Type
- single nucleotide variant
- Location
- chr22:36480577 (GRCh38)
- Gene constraint
- LOEUF 1.358 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 3 PDB
- Residue 87
- the thioredoxin domain
Similar variants
- TXN2 p.Ile126Val Uncertain significance ★★ ⚠ same type
- TXN2 p.Ile165Thr Uncertain significance ★★ ⚠ same type
- TXN2 p.Pro98Leu Uncertain significance ★★ ⚠ same type
- TXN2 p.Ser29Cys Uncertain significance ★★ ⚠ same type
- TXN2 c.387+30A>C Benign ★★ same type
- TXN2 c.388-99C>A Benign ★★ same type
- TXN2 p.Leu11= Benign ★★ same type
- TXN2 p.Pro98= Benign/Likely 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/txn2-p-ala87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown