RAX2 p.Ala170=
c.510C>T · rs941485794 · VCV1593470
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00822%, afr)
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 2.1 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 4.788 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00822%
African / African-American · 6/72,966 alleles
Filtering AF
0.00355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00244%
Overall
0.000391%
6/1,535,336 alleles · very rare
exomes 0/1,383,084 · genomes 6/152,252 · joint denominator
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.Ala170=
- Coding
- c.510C>T
- MANE Select
- NM_001319074
- dbSNP
- rs941485794
- Type
- single nucleotide variant
- Location
- chr19:3770666 (GRCh38)
- Gene constraint
- LOEUF 1.525 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 71.72
Similar variants
- RAX2 p.Ala170Val 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
- RAX2 p.Ala164Val 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-ala170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown