Is FLT3 p.Asp593del (c.1777_1779del) pathogenic?

FLT3 p.Asp593del (c.17771779del) is classified Pathogenic in FLT3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2004-05-01). Absent from gnomAD; Associated with acute lymphoblastic leukemia.

What condition is associated with FLT3 p.Asp593del (c.1777_1779del)?

FLT3 p.Asp593del (c.1777_1779del) is associated with acute lymphoblastic leukemia (ClinVar).

How common is FLT3 p.Asp593del (c.1777_1779del) in the general population?

FLT3 p.Asp593del (c.1777_1779del) is absent from gnomAD (gnomAD).

FLT3 p.Asp593del

c.1777_1779del · rs587776834 · VCV16278

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

acute lymphoblastic leukemia

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 11	GERP 1.2, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FLT3
Protein: p.Asp593del
Coding: c.1777_1779del
MANE Select: NM_004119
dbSNP: rs587776834
Type: Deletion
Location: chr13:28034140 (GRCh38)
Gene constraint: LOEUF 0.468 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.19 · 11 PDB
Residue 593: the 'important for normal regulation of the kinase activity and for maintaining the kinase in an inactive state in the absence of bound ligand' region

Full FLT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

acute lymphoblastic leukemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FLT3 p.Asp835Tyr Pathogenic ⚠ same condition
FLT3 p.Asp835Val Pathogenic ⚠ same condition
FLT3 c.1309+106del Benign ★ same type
FLT3 c.2418+38_2418+39del Benign ★ same type
FLT3 p.Asp835del 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/flt3-p-asp593del (accessed [today's date]).

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