AXL p.Asp558=
c.1674C>T · rs771425371 · VCV1594472
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, amr)
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 -6.4 | GERP -3.7 |
| Overall | ||
| CADD | 4.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,914 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00296%
Overall
0.00248%
40/1,613,576 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 9,986 |
| Finnishnot grpmax-eligible | 0.00625% | 16,007 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,824 |
| African / African-American | 0.00401% | 24,961 |
| European (non-Finnish) | 0.00195% | 51,298 |
| South Asian | 0.0011% | 91,012 |
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.Asp558=
- Coding
- c.1674C>T
- MANE Select
- NM_021913
- dbSNP
- rs771425371
- Type
- single nucleotide variant
- Location
- chr19:41248783 (GRCh38)
- Gene constraint
- LOEUF 0.625 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.57 · 4 PDB
- Residue 558
- a β-strand; the protein kinase domain
Similar variants
- AXL p.Arg217His Uncertain significance ★★ ⚠ same type
- AXL p.Glu818Lys Uncertain significance ★★ same type
- AXL p.Pro833Arg Uncertain significance ★★ ⚠ same type
- AXL c.1135-238C>T Benign ★★ same type
- AXL c.1285+62C>G Benign ★★ same type
- AXL c.1286-159G>A Benign ★★ same type
- AXL c.1286-185C>T Benign ★★ same type
- AXL c.1286-59G>A Benign ★★ 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/axl-p-asp558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown