REN p.Thr164=
c.492C>T · rs780253159 · VCV2887956
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0579%, eas)
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 -0.94 | GERP -3 |
| Overall | ||
| CADD | 1.407 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0579%
East Asian · 26/44,870 alleles
Filtering AF
0.0405%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0347%
Overall
0.00255%
41/1,609,778 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0579% | 1,726 |
| South Asian | 0.0044% | 22,749 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,370 |
| European (non-Finnish) | 0.00085% | 117,609 |
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.Thr164=
- Coding
- c.492C>T
- MANE Select
- NM_001363642 · reported on NM_000537
- dbSNP
- rs780253159
- Type
- single nucleotide variant
- Location
- chr1:204160560 (GRCh38)
- Structure
- AlphaFold pLDDT 85.00
Similar variants
- REN p.Thr164Asn Uncertain significance ★★ ⚠ same residue
- KCTD11 p.Asn164Lys 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-thr164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown