RIT1 p.Ala77=
c.231T>C · rs144170253 · VCV701984
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 0.48 | GERP -3, phastCons 0.83 |
| Overall | ||
| CADD | 7.625 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.000373%
6/1,609,568 alleles · ultra-rare
exomes 1/1,457,364 · genomes 5/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| African / African-American | 0.00668% | 14,970 |
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.Ala77=
- Coding
- c.231T>C
- MANE Select
- NM_006912
- dbSNP
- rs144170253
- Type
- single nucleotide variant
- Location
- chr1:155904737 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.96 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.78 · 3 PDB
Similar variants
- RIT1 p.Ala77Gly Pathogenic/Likely pathogenic ★★ same residue
- RIT1 p.Ala77Pro Pathogenic/Likely pathogenic ★★ same residue
- RIT1 p.Ala77Ser Pathogenic/Likely pathogenic ★★ same residue
- RIT1 p.Ala77Thr Pathogenic/Likely pathogenic ★★ same residue
- RIT1 p.Ala77_Gly78dup Uncertain significance ★ same residue
- RIT1 p.Met90Val Pathogenic ★★★ ⚠ same condition
- RIT1 p.Arg123Cys Uncertain significance ★★★ same condition
- RIT1 p.Gly78Glu Uncertain significance ★★★ ⚠ 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-ala77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown