KDR p.Ala1030=
c.3090G>A · rs36114464 · VCV695502
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.64%, 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 -8.5 | GERP -5.2 |
| Overall | ||
| CADD | 1.233 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.64%
African / African-American · 2,729/75,000 alleles
Filtering AF
3.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.48%
Overall
0.202%
3,255/1,613,994 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.64% | 27 |
| Remaining individualsnot grpmax-eligible | 0.302% | 331 |
| Admixed American | 0.245% | 408 |
| Middle Eastern | 0.149% | 673 |
| Finnishnot grpmax-eligible | 0.0906% | 1,104 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,700 |
| European (non-Finnish) | 0.00924% | 10,825 |
| South Asian | 0.00659% | 15,178 |
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.Ala1030=
- Coding
- c.3090G>A
- MANE Select
- NM_002253
- dbSNP
- rs36114464
- Type
- single nucleotide variant
- Location
- chr4:55090058 (GRCh38)
- Gene constraint
- LOEUF 0.328 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67 · 54 PDB
- Residue 1030
- the protein kinase domain; a disulfide bond
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.Ala532= 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-ala1030 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown