RAI1 p.Pro331Arg
c.992C>G · VCV3652644
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.8585 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL indeterminate
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8585 | likely pathogenic |
|---|---|---|
| REVEL | 0.352 | indeterminate |
| SaProt | LLR -7.32 | tolerated |
| ⇒ AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 23.4 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- RAI1
- Protein
- p.Pro331Arg
- Coding
- c.992C>G
- MANE Select
- NM_030665
- Type
- single nucleotide variant
- Location
- chr17:17793940 (GRCh38)
- Structure
- AlphaFold pLDDT 88.58
Similar variants
- RAI1 p.Pro331Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- RAI1 p.Arg1089Ter Pathogenic ★★ same type
- RAI1 p.Arg1560Ter Pathogenic ★★ same type
- RAI1 p.Arg1561Ter Pathogenic/Likely pathogenic ★★ same type
- RAI1 p.Arg1604Ter Pathogenic ★★ same type
- RAI1 p.Arg5Ter Pathogenic/Likely pathogenic ★★ same type
- RAI1 p.Arg80Ter Pathogenic ★★ same type
- RAI1 p.Gln1766Ter Pathogenic/Likely pathogenic ★★ 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/rai1-p-pro331arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown