RAX2 p.Pro101=
c.303C>T · rs761417697 · VCV2166174
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0225%, 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 -8.2 | GERP -3.6 |
| Overall | ||
| CADD | 0.398 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0225%
South Asian · 19/84,284 alleles
Filtering AF
0.0147%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0122%
Overall
0.00169%
26/1,536,396 alleles · ultra-rare
exomes 25/1,384,264 · genomes 1/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0225% | 4,436 |
| Middle Eastern | 0.0187% | 5,340 |
| Admixed American | 0.00587% | 17,025 |
| European (non-Finnish) | 0.000261% | 382,561 |
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
- RAX2
- Protein
- p.Pro101=
- Coding
- c.303C>T
- MANE Select
- NM_001319074
- dbSNP
- rs761417697
- Type
- single nucleotide variant
- Location
- chr19:3770873 (GRCh38)
- Gene constraint
- LOEUF 1.525 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 71.72
Similar variants
- RAX2 p.Pro52Arg Likely pathogenic ★★ same type
- RAX2 c.217-12C>A Uncertain significance ★★ same type
- RAX2 c.*368C>T Uncertain significance ★★ same type
- RAX2 p.Ala105Val Uncertain significance ★★ ⚠ same type
- RAX2 p.Ala109Thr Uncertain significance ★★ ⚠ same type
- RAX2 p.Ala160Val Uncertain significance ★★ ⚠ same type
- RAX2 p.Ala164Val Uncertain significance ★★ ⚠ same type
- RAX2 p.Ala180Pro 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/rax2-p-pro101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown