Is TXNRD2 p.Cys86= (c.258C>T) pathogenic?

TXNRD2 p.Cys86= (c.258C>T) is classified Likely benign in TXNRD2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-14). Ultra-rare (popmax 0.0187%, sas); Associated with Cardiovascular phenotype.

What condition is associated with TXNRD2 p.Cys86= (c.258C>T)?

TXNRD2 p.Cys86= (c.258C>T) is associated with Cardiovascular phenotype, dilated cardiomyopathy (ClinVar).

How common is TXNRD2 p.Cys86= (c.258C>T) in the general population?

TXNRD2 p.Cys86= (c.258C>T) is ultra-rare (popmax 0.0187%, sas) (gnomAD).

TXNRD2 p.Cys86=

c.258C>T · rs746744099 · VCV1793488

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0187%, sas)

Conditions

Cardiovascular phenotype

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 -2.5	GERP -3
Overall
CADD	5.359	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0187% South Asian · 17/91,060 alleles

Filtering AF 0.0118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00976%

Overall 0.00738% 119/1,611,628 alleles · ultra-rare exomes 114/1,459,962 · genomes 5/151,666 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0187%	5,356
European (non-Finnish)	0.00848%	11,799
Remaining individualsnot grpmax-eligible	0.0032%	31,222

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: TXNRD2
Protein: p.Cys86=
Coding: c.258C>T
MANE Select: NM_006440
dbSNP: rs746744099
Type: single nucleotide variant
Location: chr22:19918976 (GRCh38)
Gene constraint: LOEUF 1.18 · pLI <0.01 (gnomAD)
Residue 86: a disulfide bond

Full TXNRD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy

Similar variants

TXNRD2 c.104-1G>A Uncertain significance ★★ same condition
TXNRD2 c.104-3C>G Uncertain significance ★★ same condition
TXNRD2 c.1086+4C>T Uncertain significance ★★ same condition
TXNRD2 c.1087-2A>G Uncertain significance ★★ same condition
TXNRD2 c.1182+5G>A Uncertain significance ★★ same condition
TXNRD2 c.1348-2A>G Uncertain significance ★★ same condition
TXNRD2 c.1348-9G>A Uncertain significance ★★ same condition
TXNRD2 c.1445+5G>C Uncertain significance ★★ same condition

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/txnrd2-p-cys86 (accessed [today's date]).

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