RIGI p.Pro382=
c.1146G>A · rs151092988 · VCV1574662
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0307%, 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 -1.9 | GERP -3.9 |
| Overall | ||
| CADD | 6.862 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0307%
South Asian · 28/91,076 alleles
Filtering AF
0.0218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0188%
Overall
0.0104%
168/1,613,906 alleles · ultra-rare
exomes 142/1,461,702 · genomes 26/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0307% | 3,253 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,166 |
| Admixed American | 0.0167% | 6,001 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.00915% | 10,925 |
| African / African-American | 0.00667% | 15,002 |
| East Asian | 0.00223% | 44,880 |
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.Pro382=
- Coding
- c.1146G>A
- MANE Select
- NM_014314
- dbSNP
- rs151092988
- Type
- single nucleotide variant
- Location
- chr9:32488011 (GRCh38)
- Structure
- AlphaFold pLDDT 85.40 · 44 PDB
- Residue 382
- the helicase atp-binding domain; the 'interaction with zc3hav1' region; an α-helix
Similar variants
- RIGI p.Pro382Ala Uncertain significance ★ ⚠ same residue
- RIGI p.Pro382Gln Uncertain significance ★ ⚠ same residue
- RIGI p.Pro382Leu 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
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-pro382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown