KDR p.Ser68=
c.204T>C · rs141641290 · VCV695647
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.26%, 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 -1.3 | GERP -4.9 |
| Overall | ||
| CADD | 0.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.26%
African / African-American · 1,694/74,996 alleles
Filtering AF
2.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.13%
Overall
0.15%
2,419/1,614,044 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.26% | 44 |
| Middle Eastern | 0.512% | 195 |
| Remaining individualsnot grpmax-eligible | 0.242% | 414 |
| Admixed American | 0.235% | 425 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0642% | 1,558 |
| European (non-Finnish) | 0.0318% | 3,147 |
| Finnishnot grpmax-eligible | 0.00937% | 10,671 |
| East Asian | 0.00223% | 44,870 |
| South Asian | 0.0011% | 91,070 |
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.Ser68=
- Coding
- c.204T>C
- MANE Select
- NM_002253
- dbSNP
- rs141641290
- Type
- single nucleotide variant
- Location
- chr4:55118758 (GRCh38)
- Gene constraint
- LOEUF 0.328 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.67 · 54 PDB
- Residue 68
- the ig-like c2-type 1 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.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-ser68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown