TANGO2 p.Pro79=
c.237G>A · rs775546059 · VCV1557162
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0347%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.024 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -8.2 | GERP -3.1 |
| Overall | ||
| CADD | 1.411 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0347%
Middle Eastern · 2/5,760 alleles
Filtering AF
0.0061%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00252%
Overall
0.00069%
11/1,593,480 alleles · ultra-rare
exomes 11/1,441,252 · genomes 0/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0347% | 2,880 |
| East Asian | 0.00454% | 22,007 |
| Admixed American | 0.00176% | 56,956 |
| African / African-American | 0.00134% | 74,674 |
| European (non-Finnish) | 0.000427% | 234,024 |
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
- TANGO2
- Protein
- p.Pro79=
- Coding
- c.237G>A
- MANE Select
- NM_152906
- dbSNP
- rs775546059
- Type
- single nucleotide variant
- Location
- chr22:20052556 (GRCh38)
- Gene constraint
- LOEUF 0.914 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.43 · 3 PDB
- Residue 79
- a UniProt-annotated variant site (in mecrcn)
Similar variants
- TANGO2 p.Pro79Leu Uncertain significance ★★ ⚠ same residue
- TANGO2 p.Pro79Arg Uncertain significance ★ ⚠ same residue
- 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
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-pro79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown