TXN2 p.Gln36=
c.108A>G · rs776346675 · VCV2959403
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, 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 -0.54 | GERP -3 |
| Overall | ||
| CADD | 4.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,050 alleles
Filtering AF
0.00919%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00735%
Overall
0.00167%
27/1,613,952 alleles · ultra-rare
exomes 24/1,461,838 · genomes 3/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,050 |
| South Asian | 0.0154% | 6,506 |
| African / African-American | 0.00534% | 18,726 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| European (non-Finnish) | 0.000508% | 196,668 |
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.Gln36=
- Coding
- c.108A>G
- MANE Select
- NM_012473
- dbSNP
- rs776346675
- Type
- single nucleotide variant
- Location
- chr22:36480730 (GRCh38)
- Gene constraint
- LOEUF 1.358 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 3 PDB
Similar variants
- TXN2 p.Gln36Ter Uncertain significance ★ same residue
- 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
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-gln36 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown