KDR p.Ala379=
c.1137G>A · rs201755957 · VCV698917
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0132%, sas)
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 1.5 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 9.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0132%
South Asian · 12/91,074 alleles
Filtering AF
0.00751%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.00775%
125/1,613,734 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0132% | 7,589 |
| Admixed American | 0.0117% | 8,566 |
| European (non-Finnish) | 0.00822% | 12,164 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,800 |
| African / African-American | 0.00668% | 14,966 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
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.Ala379=
- Coding
- c.1137G>A
- MANE Select
- NM_002253
- dbSNP
- rs201755957
- Type
- single nucleotide variant
- Location
- chr4:55110521 (GRCh38)
- Gene constraint
- LOEUF 0.328 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67 · 54 PDB
- Residue 379
- a β-strand; the ig-like c2-type 4 domain
Similar variants
- KDR p.Ala379Val Uncertain significance ★★ ⚠ same residue
- 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.Ala532= Benign ★★ same type
- KDR p.Arg842His Likely benign ★★ ⚠ same type
- KDR p.Cys482Arg Likely 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-ala379 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown