FLT4 p.Ser1289=
c.3867C>T · rs34371546 · VCV695503
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.99%, afr)
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 5.1 | GERP -0.97, phastCons 1 |
| Overall | ||
| CADD | 3.269 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.99%
African / African-American · 2,240/75,038 alleles
Filtering AF
2.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.84%
Overall
0.16%
2,579/1,614,132 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.99% | 33 |
| Admixed American | 0.315% | 318 |
| Remaining individualsnot grpmax-eligible | 0.213% | 470 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.00329% | 30,359 |
| European (non-Finnish) | 0.000932% | 107,272 |
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
- FLT4
- Protein
- p.Ser1289=
- Coding
- c.3867C>T
- MANE Select
- NM_182925
- dbSNP
- rs34371546
- Type
- single nucleotide variant
- Location
- chr5:180608994 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.82 · 2 PDB
- Residue 1289
- a UniProt-annotated variant site (in chtd7)
Similar variants
- FLT4 p.Ser1289Arg Uncertain significance ★ ⚠ same residue
- FLT4 p.Arg1041Gln Pathogenic/Likely pathogenic ★★ same type
- FLT4 p.Arg1041Trp Pathogenic/Likely pathogenic ★★ same type
- FLT4 p.Arg318Ter Pathogenic/Likely pathogenic ★★ same type
- FLT4 p.Gly1131Ser Pathogenic/Likely pathogenic ★★ same type
- FLT4 p.Gly857Arg Pathogenic ★★ same type
- FLT4 p.Pro1137Leu Likely pathogenic ★★ same type
- FLT4 p.Ala702Ser Uncertain significance ★★ ⚠ 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/flt4-p-ser1289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown