RAX2 p.Arg79=
c.235C>A · rs1294461966 · VCV1359113
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0148%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.231 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.41 | GERP -3.6, phastCons 0.006 |
| Overall | ||
| CADD | 5.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0148%
Admixed American · 8/54,040 alleles
Filtering AF
0.00734%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00528%
Overall
0.000576%
9/1,561,956 alleles · ultra-rare
exomes 7/1,409,776 · genomes 2/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0148% | 6,755 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 61,084 |
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.Arg79=
- Coding
- c.235C>A
- MANE Select
- NM_001319074
- dbSNP
- rs1294461966
- Type
- single nucleotide variant
- Location
- chr19:3770941 (GRCh38)
- Gene constraint
- LOEUF 1.525 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 71.72
- Residue 79
- a DNA-binding region
Similar variants
- RAX2 p.Arg79Trp Uncertain significance ★★ ⚠ same residue
- RAX2 p.Arg79Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- RAX2 p.Arg79Pro Uncertain significance ★ ⚠ same residue
- 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
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-arg79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown