RTEL1 p.Pro107fs
c.320del · VCV4060914
Likely pathogenic
Multiple submitters
Classification
Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
dyskeratosis congenita
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 35 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- RTEL1
- Protein
- p.Pro107fs
- Coding
- c.320del
- MANE Select
- NM_001283009
- Type
- Deletion
- Location
- chr20:63661866 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.64 · 3 PDB
- Residue 107
- the helicase atp-binding domain
Disease context
dyskeratosis congenita — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Dyskeratosis congenita (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- Adolescent, Adult, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- RTEL1 c.1236_1266+47del Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 p.Arg879fs Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 p.Gln1187fs Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 p.Leu1112fs Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 p.Leu938fs Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 p.Ser863fs Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 c.1192-9del Benign/Likely benign ★★ same condition
- RTEL1 c.2993-8_2993-6del Benign/Likely benign ★★ 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-pro107fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown