KDR p.Ala532=
c.1596G>A · rs138803814 · VCV695646
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.824%, 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 -10 | GERP -4.8 |
| Overall | ||
| CADD | 3.139 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.824%
African / African-American · 618/74,980 alleles
Filtering AF
0.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.749%
Overall
0.0438%
707/1,613,510 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.824% | 121 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,715 |
| Admixed American | 0.0267% | 3,750 |
| East Asian | 0.0178% | 5,610 |
| Middle Eastern | 0.0165% | 6,052 |
| European (non-Finnish) | 0.00348% | 28,769 |
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
- KDR
- Protein
- p.Ala532=
- Coding
- c.1596G>A
- MANE Select
- NM_002253
- dbSNP
- rs138803814
- Type
- single nucleotide variant
- Location
- chr4:55105881 (GRCh38)
- Gene constraint
- LOEUF 0.328 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67 · 54 PDB
- Residue 532
- a β-strand; the ig-like c2-type 5 domain
Similar variants
- KDR p.Ala379Val Uncertain significance ★★ ⚠ same type
- KDR p.Ala757Gly Uncertain significance ★★ ⚠ same type
- KDR p.Asp832His Uncertain significance ★★ ⚠ same type
- KDR p.Val416Ala Uncertain significance ★★ ⚠ same type
- KDR p.Ala1030= Benign ★★ same type
- KDR p.Arg842His Likely benign ★★ ⚠ same type
- KDR p.Cys482Arg Likely benign ★★ same type
- KDR p.Glu372Asp 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/kdr-p-ala532 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown