Is TXN2 p.Ala12= (c.36C>T) pathogenic?

TXN2 p.Ala12= (c.36C>T) is classified Likely benign in TXN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-12). Absent from gnomAD v4.1.

How common is TXN2 p.Ala12= (c.36C>T) in the general population?

TXN2 p.Ala12= (c.36C>T) is absent from gnomAD v4.1 (gnomAD).

TXN2 p.Ala12=

c.36C>T · VCV3650965

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 3.8	GERP -1.1, phastCons 1
Overall
CADD	12.07	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TXN2
Protein: p.Ala12=
Coding: c.36C>T
MANE Select: NM_012473
Type: single nucleotide variant
Location: chr22:36480802 (GRCh38)
Gene constraint: LOEUF 1.358 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.10 · 3 PDB

Full TXN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TXN2 p.Ala12Val 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-ala12 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown