RAX2 p.Ala62=
c.186C>A · rs775483414 · VCV1118617
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0425%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.4 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.42, phastCons 0.99 |
| Overall | ||
| CADD | 9.266 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0425%
East Asian · 19/44,708 alleles
Filtering AF
0.0278%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0231%
Overall
0.00162%
26/1,608,364 alleles · ultra-rare
exomes 24/1,456,190 · genomes 2/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0425% | 2,353 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,768 |
| South Asian | 0.00444% | 22,511 |
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.Ala62=
- Coding
- c.186C>A
- MANE Select
- NM_001319074
- dbSNP
- rs775483414
- Type
- single nucleotide variant
- Location
- chr19:3771557 (GRCh38)
- Gene constraint
- LOEUF 1.525 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 71.72
- Residue 62
- a DNA-binding region
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-ala62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown