Is ABL1 p.Lys689del (c.2062AAG[1]) pathogenic?

ABL1 p.Lys689del (c.2062AAG[1]) is classified Uncertain significance in ABL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-23). Very rare (popmax 0.000593%, nfe).

How common is ABL1 p.Lys689del (c.2062AAG[1]) in the general population?

ABL1 p.Lys689del (c.2062AAG[1]) is very rare (popmax 0.000593%, nfe) (gnomAD).

ABL1 p.Lys689del

c.2062AAG[1] · VCV3698392

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000593%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000593% European (non-Finnish) · 7/1,179,758 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.00048% 7/1,459,852 alleles · very rare

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.Lys689del
Coding: c.2062AAG[1]
MANE Select: NM_005157
Type: Microsatellite
Location: chr9:130884351 (GRCh38)
Gene constraint: LOEUF 0.19 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.68 · 85 PDB
Residue 689: the 'disordered' region

Full ABL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABL1 p.Glu704del Uncertain significance ★ same type
ABL1 p.Leu1012fs Uncertain significance ★ same type
ABL1 p.Lys609_Thr610insLys Uncertain significance ★ same type
ABL1 p.Lys609del Conflicting classifications of pathogenicity ★ same type
ABL1 c.908-7_908-5del Likely 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/abl1-p-lys689del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown