TELO2 p.Glu539=
c.1617G>A · rs375073875 · VCV791644
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.173%, nfe)
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 1.5 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 4.485 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.173%
European (non-Finnish) · 2,032/1,177,748 alleles
Filtering AF
0.166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.164%
Overall
0.132%
2,120/1,605,442 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.173% | 580 |
| Remaining individualsnot grpmax-eligible | 0.079% | 1,266 |
| Admixed American | 0.0253% | 3,949 |
| African / African-American | 0.0227% | 4,411 |
| Finnishnot grpmax-eligible | 0.00486% | 20,565 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00341% | 29,330 |
| East Asian | 0.00224% | 44,628 |
| South Asian | 0.00223% | 44,911 |
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.Glu539=
- Coding
- c.1617G>A
- MANE Select
- NM_016111
- dbSNP
- rs375073875
- Type
- single nucleotide variant
- Location
- chr16:1502368 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.74 · 4 PDB
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-glu539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown