ABL1 p.Glu499=
c.1497A>G · rs2227985 · VCV1596488
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 17.7%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.96 | GERP -4.3 |
| Overall | ||
| CADD | 3.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
17.7%
African / African-American · 13,295/74,952 alleles
Filtering AF
17.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.4%
Overall
7.46%
120,353/1,613,902 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 17.7% | 6 |
| Middle Eastern | 10.6% | 9 |
| European (non-Finnish) | 7.75% | 13 |
| Remaining individualsnot grpmax-eligible | 7.74% | 13 |
| Ashkenazi Jewishnot grpmax-eligible | 6.86% | 15 |
| Amishnot grpmax-eligible | 5.81% | 17 |
| Admixed American | 5.68% | 18 |
| Finnishnot grpmax-eligible | 3.65% | 27 |
| South Asian | 2.54% | 39 |
| East Asian | 0.0156% | 6,410 |
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.Glu499=
- Coding
- c.1497A>G
- MANE Select
- NM_005157
- dbSNP
- rs2227985
- Type
- single nucleotide variant
- Location
- chr9:130880141 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 85 PDB
- Residue 499
- a β-strand
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-glu499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown