RIGI p.Asp822=
c.2466C>T · rs149989209 · VCV1137919
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.99 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.049 | GERP -3.6 |
| Overall | ||
| CADD | 7.294 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.00155%
25/1,613,484 alleles · ultra-rare
exomes 22/1,461,306 · genomes 3/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| East Asian | 0.00669% | 14,953 |
| South Asian | 0.0033% | 30,309 |
| Admixed American | 0.00167% | 59,844 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| African / African-American | 0.00133% | 74,954 |
| European (non-Finnish) | 0.00119% | 84,278 |
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
- RIGI
- Protein
- p.Asp822=
- Coding
- c.2466C>T
- MANE Select
- NM_014314
- dbSNP
- rs149989209
- Type
- single nucleotide variant
- Location
- chr9:32459386 (GRCh38)
- Structure
- AlphaFold pLDDT 85.40 · 44 PDB
- Residue 822
- an α-helix; the rlr ctr domain; the 'interaction with zc3hav1' region; the 'mediates interaction with rnf135' region
Similar variants
- RIGI c.1923+1G>A Uncertain significance ★★ same type
- RIGI c.954-6T>G Uncertain significance ★★ same type
- RIGI p.Ala436Val Uncertain significance ★★ ⚠ same type
- RIGI p.Ala486Thr Uncertain significance ★★ ⚠ same type
- RIGI p.Ala537Ser Uncertain significance ★★ ⚠ same type
- RIGI p.Ala537Thr Uncertain significance ★★ ⚠ same type
- RIGI p.Ala774Thr Uncertain significance ★★ ⚠ same type
- RIGI p.Arg109Cys 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/rigi-p-asp822 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown