RIGI p.Ser906=
c.2718G>A · rs751820024 · VCV2876921
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2 | GERP -4.3 |
| Overall | ||
| CADD | 6.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,872 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000496%
8/1,613,584 alleles · ultra-rare
exomes 7/1,461,506 · genomes 1/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,479 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 8.48e-05% | 1,179,736 |
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.Ser906=
- Coding
- c.2718G>A
- MANE Select
- NM_014314
- dbSNP
- rs751820024
- Type
- single nucleotide variant
- Location
- chr9:32457182 (GRCh38)
- Structure
- AlphaFold pLDDT 85.40 · 44 PDB
- Residue 906
- the rlr ctr domain; the 'interaction with zc3hav1' region; the 'mediates interaction with rnf135' region
Similar variants
- RIGI p.Ser906Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser906 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown