TELO2 p.Pro260=
c.780G>A · rs150053866 · VCV2885966
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00554%, amr)
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 -11 | GERP -4 |
| Overall | ||
| CADD | 3.597 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00554%
Admixed American · 3/54,120 alleles
Filtering AF
0.00159%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000933%
Overall
0.00102%
16/1,573,230 alleles · very rare
exomes 14/1,421,014 · genomes 2/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00554% | 18,040 |
| South Asian | 0.00466% | 21,474 |
| African / African-American | 0.00406% | 24,603 |
| Finnishnot grpmax-eligible | 0.00338% | 29,582 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 60,960 |
| European (non-Finnish) | 0.000258% | 387,039 |
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.Pro260=
- Coding
- c.780G>A
- MANE Select
- NM_016111
- dbSNP
- rs150053866
- Type
- single nucleotide variant
- Location
- chr16:1497458 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.74 · 4 PDB
- Residue 260
- a UniProt-annotated variant site (in yhfs); an α-helix
Similar variants
- TELO2 p.Pro260Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-pro260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown