REN p.Ser107=
c.321G>A · VCV3709434
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0662%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor loss, 5 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -4.8 |
| Overall | ||
| CADD | 0.355 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0662%
Middle Eastern · 4/6,044 alleles
Filtering AF
0.0226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0174%
Overall
0.00634%
102/1,608,754 alleles · ultra-rare
exomes 90/1,456,576 · genomes 12/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0662% | 1,511 |
| South Asian | 0.029% | 3,448 |
| East Asian | 0.0134% | 7,448 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,897 |
| African / African-American | 0.00801% | 12,482 |
| European (non-Finnish) | 0.00442% | 22,648 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00342% | 29,258 |
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.Ser107=
- Coding
- c.321G>A
- MANE Select
- NM_000537
- Type
- single nucleotide variant
- Location
- chr1:204161344 (GRCh38)
- Structure
- AlphaFold pLDDT 85.00
Similar variants
- REN p.Ser107Leu 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-ser107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown