FLT3 p.Pro60=
c.180G>A · rs749445819 · VCV735561
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00835%, amr)
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 -5.2 | GERP -4.4 |
| Overall | ||
| CADD | 1.631 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00835%
Admixed American · 5/59,902 alleles
Filtering AF
0.00324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00236%
38/1,611,816 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00835% | 11,980 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,151 |
| European (non-Finnish) | 0.00254% | 39,328 |
| African / African-American | 0.00134% | 74,796 |
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.Pro60=
- Coding
- c.180G>A
- MANE Select
- NM_004119
- dbSNP
- rs749445819
- Type
- single nucleotide variant
- Location
- chr13:28062055 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.19 · 11 PDB
- Residue 60
- a disulfide bond
Similar variants
- 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
- FLT3 c.165+118G>T 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-pro60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown