RTEL1 p.Val247=
c.741G>C · VCV4945848
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.3e-05%)
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 2.7 | GERP -0.13, phastCons 1 |
| Overall | ||
| CADD | 8.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.3e-05%
Overall
6.3e-05%
1/1,586,276 alleles · very rare
exomes 1/1,433,924 · genomes 0/152,352 · 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.Val247=
- Coding
- c.741G>C
- MANE Select
- NM_001283009
- Type
- single nucleotide variant
- Location
- chr20:63672597 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.64 · 3 PDB
- Residue 247
- the helicase atp-binding domain
Similar variants
- RTEL1 p.Val247Met Uncertain significance ★★ same residue
- RTEL1 c.1037+1G>T Likely pathogenic ★★ same type
- RTEL1 c.1192-2A>G Likely pathogenic ★★ same type
- RTEL1 c.1596-1G>A Likely pathogenic ★★ same type
- RTEL1 c.2142-1G>C Likely pathogenic ★★ same type
- RTEL1 c.2265+1G>T Likely pathogenic ★★ same type
- RTEL1 c.2413+1G>A Likely pathogenic ★★ same type
- RTEL1 c.2413+1G>C Pathogenic/Likely pathogenic ★★ 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/rtel1-p-val247 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown