TELO2 p.Ala835=
c.2505G>A · rs546196109 · VCV762485
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0433%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 0.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0433%
South Asian · 38/87,854 alleles
Filtering AF
0.0324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0285%
Overall
0.0064%
102/1,594,668 alleles · ultra-rare
exomes 93/1,442,376 · genomes 9/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0433% | 2,312 |
| Middle Eastern | 0.0167% | 6,002 |
| Remaining individualsnot grpmax-eligible | 0.0081% | 12,344 |
| European (non-Finnish) | 0.00444% | 22,526 |
| African / African-American | 0.00403% | 24,827 |
| Admixed American | 0.00345% | 28,946 |
| East Asian | 0.00229% | 43,686 |
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.Ala835=
- Coding
- c.2505G>A
- MANE Select
- NM_016111
- dbSNP
- rs546196109
- Type
- single nucleotide variant
- Location
- chr16:1509927 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.74 · 4 PDB
Similar variants
- TELO2 p.Ala835Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
- TELO2 p.Ala835Thr Uncertain significance ★ ⚠ same residue
- TELO2 p.Ala835Val Uncertain significance ★ ⚠ 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
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-ala835 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown