RTEL1 p.Arg762=
c.2286G>C · rs2090704904 · VCV2932782
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Conditions
2
pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3
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 -0.067 | GERP -2.5 |
| Overall | ||
| CADD | 0.646 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,786 alleles
Overall
6.22e-05%
1/1,608,398 alleles · very rare
exomes 0/1,456,324 · genomes 1/152,074 · 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.Arg762=
- Coding
- c.2286G>C
- MANE Select
- NM_001283009
- dbSNP
- rs2090704904
- Type
- single nucleotide variant
- Location
- chr20:63690314 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.64 · 3 PDB
- Residue 762
- the 'disordered' region
Similar variants
- RTEL1 p.Arg762Gln Uncertain significance ★★ ⚠ same residue
- RTEL1 p.Arg762Trp Uncertain significance ★★ ⚠ same residue
- RTEL1 p.Arg762fs Likely pathogenic ★ 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
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-arg762 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown