Is FLT3 p.Ala813= (c.2439C>T) pathogenic?

FLT3 p.Ala813= (c.2439C>T) is classified Likely benign in FLT3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-30). Ultra-rare (popmax 0.0178%, eas); Associated with FLT3-related disorder.

What condition is associated with FLT3 p.Ala813= (c.2439C>T)?

FLT3 p.Ala813= (c.2439C>T) is associated with FLT3-related disorder (ClinVar).

How common is FLT3 p.Ala813= (c.2439C>T) in the general population?

FLT3 p.Ala813= (c.2439C>T) is ultra-rare (popmax 0.0178%, eas) (gnomAD).

FLT3 p.Ala813=

c.2439C>T · rs141860068 · VCV3053518

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0178%, eas)

Conditions

FLT3-related disorder

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 -9.9	GERP -4.7
Overall
CADD	0.182	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0178% East Asian · 8/44,886 alleles

Filtering AF 0.00883% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00641%

Overall 0.00607% 98/1,614,052 alleles · ultra-rare exomes 92/1,461,826 · genomes 6/152,226 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0178%	5,611
European (non-Finnish)	0.00703%	14,217
Remaining individualsnot grpmax-eligible	0.0048%	20,833
African / African-American	0.00267%	37,507
Admixed American	0.00167%	60,004
South Asian	0.0011%	91,070

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: FLT3
Protein: p.Ala813=
Coding: c.2439C>T
MANE Select: NM_004119
dbSNP: rs141860068
Type: single nucleotide variant
Location: chr13:28018569 (GRCh38)
Gene constraint: LOEUF 0.468 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.19 · 11 PDB
Residue 813: the protein kinase domain

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

Disease context

FLT3-related disorder

Similar variants

FLT3 p.Ser446Leu Likely benign same condition
FLT3 p.Val95= Likely benign same condition
FLT3 p.Tyr597_Glu598insAspValAspPheArgGluTyr Pathogenic ★ same condition
FLT3 c.1205+56C>T Benign ★★ same type
FLT3 c.1310-3T>C Benign ★★ same type
FLT3 c.1418+75A>G Benign ★★ same type
FLT3 c.1418+81A>G Benign ★★ same type
FLT3 c.1419-15T>C 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/flt3-p-ala813 (accessed [today's date]).

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