ABL1 p.Ala269=
c.807C>T · rs148722778 · VCV1567710
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0328%, nfe)
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 -8.6 | GERP -4.3 |
| Overall | ||
| CADD | 4.579 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0328%
European (non-Finnish) · 385/1,173,880 alleles
Filtering AF
0.0301%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.029%
Overall
0.0255%
410/1,605,342 alleles · ultra-rare
exomes 380/1,453,098 · genomes 30/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0328% | 3,049 |
| Remaining individualsnot grpmax-eligible | 0.0161% | 6,211 |
| East Asian | 0.00895% | 11,179 |
| African / African-American | 0.00534% | 18,726 |
| South Asian | 0.00444% | 22,531 |
| Finnishnot grpmax-eligible | 0.00313% | 31,920 |
| Admixed American | 0.00167% | 59,732 |
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
- ABL1
- Protein
- p.Ala269=
- Coding
- c.807C>T
- MANE Select
- NM_005157
- dbSNP
- rs148722778
- Type
- single nucleotide variant
- Location
- chr9:130863020 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 85 PDB
- Residue 269
- a β-strand; the protein kinase domain
Similar variants
- ABL1 p.Ala337Thr Pathogenic ★★ ⚠ same type
- ABL1 p.Ala433Thr Likely pathogenic ★★ ⚠ same type
- ABL1 p.Asp504Gly Likely pathogenic ★★ ⚠ same type
- ABL1 p.Glu509Lys Pathogenic/Likely pathogenic ★★ same type
- ABL1 p.Gly254Arg Pathogenic/Likely pathogenic ★★ same type
- ABL1 p.Pro230Leu Likely pathogenic ★★ ⚠ same type
- ABL1 p.Trp99Arg Likely pathogenic ★★ same type
- ABL1 p.Tyr226Cys Pathogenic/Likely pathogenic ★★ ⚠ 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/abl1-p-ala269 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown