RTEL1 p.Arg1026=
c.3078G>A · rs2090915065 · VCV2162980
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.51e-05%, nfe)
Conditions
3
Inborn genetic diseases
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 0.38 | GERP -2.5 |
| Overall | ||
| CADD | 3.929 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.51e-05%
European (non-Finnish) · 1/1,174,424 alleles
Overall
6.23e-05%
1/1,606,014 alleles · very rare
exomes 1/1,453,700 · genomes 0/152,314 · joint denominator
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
- RTEL1
- Protein
- p.Arg1026=
- Coding
- c.3078G>A
- MANE Select
- NM_001283009
- dbSNP
- rs2090915065
- Type
- single nucleotide variant
- Location
- chr20:63694457 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.64 · 3 PDB
- Residue 1026
- the 'disordered' region
Similar variants
- RTEL1 p.Arg1026Met Uncertain significance ★★ ⚠ same residue
- RTEL1 p.Arg1026Trp Uncertain significance ★ ⚠ same residue
- RTEL1 c.1037+1G>T Likely pathogenic ★★ same condition
- RTEL1 c.1192-2A>G Likely pathogenic ★★ same condition
- RTEL1 c.1596-1G>A Likely pathogenic ★★ same condition
- RTEL1 c.2142-1G>C Likely pathogenic ★★ same condition
- RTEL1 c.2265+1G>T Likely pathogenic ★★ same condition
- RTEL1 c.2413+1G>A Likely pathogenic ★★ same condition
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/rtel1-p-arg1026 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown