RAX2 p.Pro18=
c.54G>A · rs367658021 · VCV1019155
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0142%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.011 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -4 |
| Overall | ||
| CADD | 1.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0142%
European (non-Finnish) · 167/1,179,822 alleles
Filtering AF
0.0124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0117%
Overall
0.0111%
179/1,611,950 alleles · ultra-rare
exomes 172/1,459,816 · genomes 7/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0142% | 7,065 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,807 |
| African / African-American | 0.004% | 24,971 |
| Admixed American | 0.00334% | 29,969 |
| South Asian | 0.0033% | 30,336 |
| Finnishnot grpmax-eligible | 0.0016% | 62,422 |
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.Pro18=
- Coding
- c.54G>A
- MANE Select
- NM_001319074
- dbSNP
- rs367658021
- Type
- single nucleotide variant
- Location
- chr19:3771689 (GRCh38)
- Gene constraint
- LOEUF 1.525 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 71.72
- Residue 18
- the 'disordered' region
Similar variants
- RAX2 p.Pro18Leu Uncertain significance ★★ ⚠ same residue
- RAX2 p.Pro18fs 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
- RAX2 p.Ala160Val 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-pro18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown