RIT1 p.Arg86=
c.258G>A · rs909585898 · VCV1979660
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Conditions
1
Noonan syndrome 8
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 -0.28 | GERP -4.2, phastCons 0.19 |
| Overall | ||
| CADD | 8.621 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,894 alleles
Overall
6.2e-05%
1/1,613,574 alleles · very rare
exomes 0/1,461,448 · genomes 1/152,126 · joint denominator
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
- RIT1
- Protein
- p.Arg86=
- Coding
- c.258G>A
- MANE Select
- NM_006912
- dbSNP
- rs909585898
- Type
- single nucleotide variant
- Location
- chr1:155904482 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.96 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.78 · 3 PDB
- Residue 86
- an α-helix
Similar variants
- RIT1 p.Arg86Trp Uncertain significance ★★ ⚠ same residue
- RIT1 p.Arg86Gln Uncertain significance ★ ⚠ same residue
- RIT1 p.Met90Val Pathogenic ★★★ ⚠ same condition
- RIT1 p.Arg123Cys Uncertain significance ★★★ same condition
- RIT1 p.Gly78Glu Uncertain significance ★★★ ⚠ same condition
- RIT1 p.Ala57Gly Pathogenic/Likely pathogenic ★★ ⚠ same condition
- RIT1 p.Ala77Gly Pathogenic/Likely pathogenic ★★ same condition
- RIT1 p.Ala77Pro Pathogenic/Likely pathogenic ★★ same condition
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/rit1-p-arg86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown