FLT1 p.Pro1323=
c.3969G>A · rs142100250 · VCV713356
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.101%, 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 -3.1 | GERP -4.9 |
| Overall | ||
| CADD | 0.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.101%
African / African-American · 76/74,900 alleles
Filtering AF
0.083%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0763%
Overall
0.00564%
91/1,613,058 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.101% | 986 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| Admixed American | 0.00333% | 29,991 |
| Finnishnot grpmax-eligible | 0.00158% | 63,282 |
| South Asian | 0.0011% | 91,042 |
| European (non-Finnish) | 0.000509% | 196,655 |
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
- FLT1
- Protein
- p.Pro1323=
- Coding
- c.3969G>A
- MANE Select
- NM_002019
- dbSNP
- rs142100250
- Type
- single nucleotide variant
- Location
- chr13:28303215 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.86 · 12 PDB
Similar variants
- FLT1 p.Asp6Asn Benign ★★ same type
- FLT1 p.Cys107= Likely benign ★★ same type
- FLT1 p.Ile548Met Likely benign ★★ same type
- FLT1 p.Leu492= Benign ★★ same type
- FLT1 p.Met938Val Likely benign ★★ same type
- FLT1 p.Pro1068= Benign ★★ same type
- FLT1 p.Pro1201Leu Likely benign ★★ same type
- FLT1 p.Thr260= 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/flt1-p-pro1323 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown