TANGO2 p.Thr238=
c.714C>G · rs1602439392 · VCV755985
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. | ||
| REVEL | 0.188 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.23 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.087 | GERP -2.5, phastCons 0.91 |
| Overall | ||
| CADD | 6.428 | 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
- TANGO2
- Protein
- p.Thr238=
- Coding
- c.714C>G
- MANE Select
- NM_152906
- dbSNP
- rs1602439392
- Type
- single nucleotide variant
- Location
- chr22:20064545 (GRCh38)
- Gene constraint
- LOEUF 0.914 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.43 · 3 PDB
- Residue 238
- a UniProt-annotated variant site (in mecrcn); a UniProt-annotated variant site (in mecrcn; delayed er-to-golgi transport; altered mitochondrial morphology); a UniProt-annotated variant site (in mecrcn; uncertain significance); a β-strand
Similar variants
- TANGO2 c.451+2T>A Pathogenic/Likely pathogenic ★★ same type
- TANGO2 c.57-1G>C Pathogenic/Likely pathogenic ★★ same type
- TANGO2 c.605+1G>A Pathogenic/Likely pathogenic ★★ same type
- TANGO2 c.711-3C>G Pathogenic/Likely pathogenic ★★ same type
- TANGO2 p.Arg140Ter Pathogenic ★★ same type
- TANGO2 p.Arg32Ter Pathogenic/Likely pathogenic ★★ same type
- TANGO2 p.Arg86Ter Pathogenic/Likely pathogenic ★★ same type
- TANGO2 p.Arg88Ter Pathogenic ★★ 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/tango2-p-thr238 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown