KDR p.Thr1152=
c.3456G>A · rs56242771 · VCV3052916
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.198%, eas)
Conditions
1
KDR-related disorder
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 -9.7 | GERP -5.5 |
| Overall | ||
| CADD | 6.633 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.198%
East Asian · 89/44,878 alleles
Filtering AF
0.165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.153%
Overall
0.00774%
125/1,614,158 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.198% | 504 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| South Asian | 0.00439% | 22,769 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.00144% | 69,413 |
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.Thr1152=
- Coding
- c.3456G>A
- MANE Select
- NM_002253
- dbSNP
- rs56242771
- Type
- single nucleotide variant
- Location
- chr4:55088922 (GRCh38)
- Gene constraint
- LOEUF 0.328 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67 · 54 PDB
- Residue 1152
- the protein kinase domain
Disease context
KDR-related disorder
Similar variants
- KDR p.Gly1092Arg Uncertain significance ⚠ same condition
- KDR c.1537-6G>A Likely benign same condition
- KDR c.3510+10C>T Likely benign same condition
- KDR c.-1G>T Benign same condition
- KDR p.Gln472His Benign same condition
- KDR p.Gly1283= Likely benign same condition
- KDR p.Ile1330Leu Benign same condition
- KDR p.Lys941= Likely benign same condition
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-thr1152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown