TXN2 p.Phe160=
c.480C>T · rs754825420 · VCV1962579
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 5.7 | GERP 0.76, phastCons 1 |
| Overall | ||
| CADD | 12.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,018 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000684%
10/1,461,638 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,003 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
| European (non-Finnish) | 0.000254% | 393,334 |
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.Phe160=
- Coding
- c.480C>T
- MANE Select
- NM_012473
- dbSNP
- rs754825420
- Type
- single nucleotide variant
- Location
- chr22:36467825 (GRCh38)
- Gene constraint
- LOEUF 1.358 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 3 PDB
- Residue 160
- the thioredoxin domain; an α-helix
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.Ala87= Likely benign ★★ same type
- TXN2 p.Leu11= 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-phe160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown