AXL p.Pro12=
c.36G>A · rs530407469 · VCV3049243
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00508%, amr)
Conditions
1
AXL-related disorder
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 0.26 | GERP -2.1, phastCons 0.011 |
| Overall | ||
| CADD | 4.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00508%
Admixed American · 3/59,074 alleles
Filtering AF
0.0024%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0021%
Overall
0.00286%
46/1,606,066 alleles · very rare
exomes 44/1,453,920 · genomes 2/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00508% | 19,691 |
| South Asian | 0.00447% | 22,383 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0034% | 29,388 |
| European (non-Finnish) | 0.00323% | 30,964 |
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
- AXL
- Protein
- p.Pro12=
- Coding
- c.36G>A
- MANE Select
- NM_021913
- dbSNP
- rs530407469
- Type
- single nucleotide variant
- Location
- chr19:41219428 (GRCh38)
- Gene constraint
- LOEUF 0.625 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.57 · 4 PDB
Disease context
AXL-related disorder
Similar variants
- AXL p.Pro12Leu Uncertain significance ★ ⚠ same residue
- AXL p.Arg217His Uncertain significance ★★ ⚠ same condition
- AXL p.Arg475Gln Uncertain significance ⚠ same condition
- AXL c.410-7C>T Likely benign same condition
- AXL p.Ala151= Likely benign same condition
- AXL p.Leu264= Likely benign same condition
- AXL p.Leu364= Likely benign same condition
- AXL p.Gly736_Val737insTer Uncertain significance ★ same condition
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/axl-p-pro12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown