TELO2 p.Pro643=
c.1929G>A · rs778884447 · VCV1898256
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -1.6 |
| Overall | ||
| CADD | 4.688 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,872 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00112%
18/1,613,108 alleles · very rare
exomes 18/1,460,778 · genomes 0/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00669% | 14,957 |
| South Asian | 0.00329% | 30,363 |
| European (non-Finnish) | 0.00102% | 98,333 |
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
- TELO2
- Protein
- p.Pro643=
- Coding
- c.1929G>A
- MANE Select
- NM_016111
- dbSNP
- rs778884447
- Type
- single nucleotide variant
- Location
- chr16:1505496 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.74 · 4 PDB
- Residue 643
- the 'disordered' region
Similar variants
- TELO2 c.2034+2T>C Likely pathogenic ★★ same type
- TELO2 c.2291+1G>C Likely pathogenic ★★ same type
- TELO2 p.Arg403Ter Pathogenic/Likely pathogenic ★★ same type
- TELO2 p.Arg609His Pathogenic/Likely pathogenic ★★ same type
- TELO2 p.Cys367Phe Pathogenic/Likely pathogenic ★★ same type
- TELO2 c.830+5G>T Uncertain significance ★★ same type
- TELO2 p.Ala198Val Uncertain significance ★★ ⚠ same type
- TELO2 p.Ala323Pro Uncertain significance ★★ ⚠ 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/telo2-p-pro643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown