AXL p.Ile656=
c.1968C>T · rs79369530 · VCV3038712
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.245%, 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 -2.2 | GERP -3.4 |
| Overall | ||
| CADD | 4.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.245%
East Asian · 110/44,840 alleles
Filtering AF
0.208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.194%
Overall
0.0144%
232/1,613,812 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.245% | 408 |
| African / African-American | 0.139% | 721 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| Admixed American | 0.005% | 19,993 |
| Finnishnot grpmax-eligible | 0.00156% | 63,992 |
| European (non-Finnish) | 0.000847% | 117,994 |
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.Ile656=
- Coding
- c.1968C>T
- MANE Select
- NM_021913
- dbSNP
- rs79369530
- Type
- single nucleotide variant
- Location
- chr19:41253640 (GRCh38)
- Gene constraint
- LOEUF 0.625 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.57 · 4 PDB
- Residue 656
- an α-helix; the protein kinase domain
Similar variants
- AXL p.Ile656Val Uncertain significance ★ ⚠ same residue
- 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
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-ile656 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown