TANGO2 p.Ser263=
c.789C>T · rs34082990 · VCV788628
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.53%, afr)
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 0.087 | GERP -0.96 |
| Overall | ||
| CADD | 7.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.53%
African / African-American · 1,150/75,048 alleles
Filtering AF
1.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.43%
Overall
0.0887%
1,431/1,614,162 alleles · low-frequency
exomes 768/1,461,862 · genomes 663/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.53% | 65 |
| Ashkenazi Jewishnot grpmax-eligible | 0.169% | 592 |
| Remaining individualsnot grpmax-eligible | 0.141% | 710 |
| Middle Eastern | 0.132% | 758 |
| Admixed American | 0.117% | 857 |
| European (non-Finnish) | 0.00534% | 18,730 |
| South Asian | 0.0022% | 45,540 |
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.Ser263=
- Coding
- c.789C>T
- MANE Select
- NM_152906
- dbSNP
- rs34082990
- Type
- single nucleotide variant
- Location
- chr22:20064620 (GRCh38)
- Gene constraint
- LOEUF 0.914 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.43 · 3 PDB
- Residue 263
- a UniProt-annotated variant site (in mecrcn); a UniProt-annotated variant site (in mecrcn; uncertain significance); a β-strand
Similar variants
- TANGO2 p.Ser263Phe Uncertain significance ★ ⚠ same residue
- TANGO2 p.Ser263Pro 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-ser263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown