REN p.Leu69=
c.207T>C · VCV3623449
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00305%, nfe)
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 -2.2 | GERP -4.4 |
| Overall | ||
| CADD | 0.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00305%
European (non-Finnish) · 36/1,180,030 alleles
Filtering AF
0.00223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00242%
39/1,613,980 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00305% | 32,779 |
| African / African-American | 0.00267% | 37,450 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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
- REN
- Protein
- p.Leu69=
- Coding
- c.207T>C
- MANE Select
- NM_001363642 · reported on NM_000537
- Type
- single nucleotide variant
- Location
- chr1:204162055 (GRCh38)
- Structure
- AlphaFold pLDDT 85.00
Similar variants
- KCTD11 p.Gly69Asp Uncertain significance ★ ⚠ same residue
- REN c.249+1G>A Pathogenic/Likely pathogenic ★★ same type
- REN p.Arg49Ter Pathogenic/Likely pathogenic ★★ same type
- REN p.Lys139Ter Pathogenic ★★ same type
- REN p.Ala182Thr Uncertain significance ★★ ⚠ same type
- REN p.Arg119Cys Uncertain significance ★★ ⚠ same type
- REN p.Arg119His Uncertain significance ★★ ⚠ same type
- REN p.Arg148His Uncertain significance ★★ ⚠ 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/ren-p-leu69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown