KDR p.Thr442=
c.1326G>A · rs41279537 · VCV698514
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0205%, nfe)
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 -20 | GERP -4.8 |
| Overall | ||
| CADD | 0.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0205%
European (non-Finnish) · 242/1,179,876 alleles
Filtering AF
0.0183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0175%
Overall
0.0156%
252/1,613,700 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0205% | 4,876 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,412 |
| East Asian | 0.00446% | 22,429 |
| Admixed American | 0.00167% | 59,958 |
| African / African-American | 0.00134% | 74,864 |
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.Thr442=
- Coding
- c.1326G>A
- MANE Select
- NM_002253
- dbSNP
- rs41279537
- Type
- single nucleotide variant
- Location
- chr4:55107823 (GRCh38)
- Gene constraint
- LOEUF 0.328 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67 · 54 PDB
- Residue 442
- 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.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-thr442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown