RTEL1 p.Leu229=
c.687G>A · rs2090161152 · VCV2952351
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
2
dyskeratosis congenita, autosomal recessive 5
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 3.3 | GERP 0.012, phastCons 1 |
| Overall | ||
| CADD | 7.667 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,816 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,618 alleles · very rare
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.Leu229=
- Coding
- c.687G>A
- MANE Select
- NM_001283009
- dbSNP
- rs2090161152
- Type
- single nucleotide variant
- Location
- chr20:63667541 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.64 · 3 PDB
- Residue 229
- the helicase atp-binding domain
Similar variants
- 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
- RTEL1 c.2413+1G>C Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 c.2557-2A>G 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-leu229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown