RAX p.Pro113=
c.339A>C · rs749230690 · VCV770087
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -7.8 | GERP -4.2 |
| Overall | ||
| CADD | 2.668 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,858 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000434%
7/1,613,846 alleles · very rare
exomes 5/1,461,696 · genomes 2/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,429 |
| Admixed American | 0.00333% | 30,001 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| European (non-Finnish) | 0.000169% | 589,988 |
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
- RAX
- Protein
- p.Pro113=
- Coding
- c.339A>C
- MANE Select
- NM_013435
- dbSNP
- rs749230690
- Type
- single nucleotide variant
- Location
- chr18:59272565 (GRCh38)
- Gene constraint
- LOEUF 1.197 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.10
- Residue 113
- the 'disordered' region
Similar variants
- RAX c.*1300A>G Uncertain significance ★★ same type
- RAX c.*850C>T Uncertain significance ★★ same type
- RAX p.Ala267Val Uncertain significance ★★ ⚠ same type
- RAX p.Ala72Gly Uncertain significance ★★ ⚠ same type
- RAX p.Arg110Gly Uncertain significance ★★ ⚠ same type
- RAX p.Arg166Pro Uncertain significance ★★ ⚠ same type
- RAX p.Glu96Gln Uncertain significance ★★ ⚠ same type
- RAX p.Gly237Asp 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/rax-p-pro113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown