RIT1 p.Asp173=
c.519T>C · rs1203053742 · VCV2812503
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, 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 -0.58 | GERP -3 |
| Overall | ||
| CADD | 7.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,048 alleles
Overall
6.2e-05%
1/1,614,194 alleles · very rare
exomes 1/1,461,880 · genomes 0/152,314 · 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.Asp173=
- Coding
- c.519T>C
- MANE Select
- NM_006912
- dbSNP
- rs1203053742
- Type
- single nucleotide variant
- Location
- chr1:155900529 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.96 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.78 · 3 PDB
- Residue 173
- an α-helix
Similar variants
- 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
- RIT1 p.Ala77Ser Pathogenic/Likely pathogenic ★★ same condition
- RIT1 p.Ala77Thr 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-asp173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown