RAX2 p.Pro124=
c.372C>T · VCV4939901
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0206%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.006 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6 | GERP -3.6 |
| Overall | ||
| CADD | 0.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0206%
Middle Eastern · 1/4,858 alleles
Filtering AF
0.000987%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000814%
Overall
0.00165%
25/1,519,568 alleles · ultra-rare
exomes 25/1,367,278 · genomes 0/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0206% | 4,858 |
| Finnishnot grpmax-eligible | 0.00454% | 22,011 |
| South Asian | 0.00243% | 41,210 |
| Admixed American | 0.00202% | 49,428 |
| Remaining individualsnot grpmax-eligible | 0.00169% | 59,102 |
| European (non-Finnish) | 0.00158% | 63,332 |
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.Pro124=
- Coding
- c.372C>T
- MANE Select
- NM_001319074
- Type
- single nucleotide variant
- Location
- chr19:3770804 (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-pro124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown