REN p.Thr169=
c.507G>A · rs750082768 · VCV2899513
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0318%, sas)
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 -7 | GERP -3.9 |
| Overall | ||
| CADD | 0.867 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0318%
South Asian · 29/91,084 alleles
Filtering AF
0.0228%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0196%
Overall
0.00341%
55/1,614,040 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0318% | 3,141 |
| Admixed American | 0.00833% | 12,000 |
| East Asian | 0.00445% | 22,449 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.00144% | 69,414 |
| African / African-American | 0.00133% | 74,910 |
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.Thr169=
- Coding
- c.507G>A
- MANE Select
- NM_001363642 · reported on NM_000537
- dbSNP
- rs750082768
- Type
- single nucleotide variant
- Location
- chr1:204159581 (GRCh38)
- Structure
- AlphaFold pLDDT 85.00
Similar variants
- REN p.Thr169Met Uncertain significance ★★ ⚠ same residue
- REN p.Thr169Ala 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
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-thr169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown