FLT3 p.Ser941=
c.2823G>A · rs201025099 · VCV710610
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0201%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.50 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -4.7 |
| Overall | ||
| CADD | 4.642 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0201%
East Asian · 9/44,886 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00779%
Overall
0.00211%
34/1,613,878 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0201% | 4,987 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,249 |
| African / African-American | 0.00267% | 37,506 |
| Admixed American | 0.00167% | 60,008 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 0.000932% | 107,256 |
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.Ser941=
- Coding
- c.2823G>A
- MANE Select
- NM_004119
- dbSNP
- rs201025099
- Type
- single nucleotide variant
- Location
- chr13:28014488 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.19 · 11 PDB
- Residue 941
- an α-helix; the protein kinase domain
Similar variants
- FLT3 p.Ser941Leu Uncertain significance ★ ⚠ same residue
- 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
- FLT3 c.1419-36T>A Benign ★★ same type
- FLT3 c.1597+8A>G 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/flt3-p-ser941 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown