KIF20A p.Pro8=
c.24G>A · rs201784256 · VCV1528373
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.354%, eas)
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 -0.79 | GERP -3.4 |
| Overall | ||
| CADD | 11.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.354%
East Asian · 159/44,874 alleles
Filtering AF
0.309%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.292%
Overall
0.0104%
168/1,614,004 alleles · rare
exomes 151/1,461,842 · genomes 17/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.354% | 282 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,249 |
| South Asian | 0.0022% | 45,537 |
| Admixed American | 0.00167% | 60,002 |
| European (non-Finnish) | 0.000339% | 295,003 |
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
- KIF20A
- Protein
- p.Pro8=
- Coding
- c.24G>A
- MANE Select
- NM_005733
- dbSNP
- rs201784256
- Type
- single nucleotide variant
- Location
- chr5:138179704 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.22 · 1 PDB
Similar variants
- KIF20A p.Pro8Leu Uncertain significance ★★ ⚠ same residue
- KIF20A p.Ala106Ser Uncertain significance ★★ ⚠ same type
- KIF20A p.Ala761Thr Uncertain significance ★★ ⚠ same type
- KIF20A p.Arg218Gln Uncertain significance ★★ ⚠ same type
- KIF20A p.Arg250Gln Uncertain significance ★★ ⚠ same type
- KIF20A p.Arg282Gln Uncertain significance ★★ ⚠ same type
- KIF20A p.Arg298His Uncertain significance ★★ ⚠ same type
- KIF20A p.Arg298Pro Uncertain significance ★★ 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/kif20a-p-pro8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown