KIF2A p.Pro609=
c.1827A>G · rs750351717 · VCV2881042
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.032 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 9.689 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,882 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000372%
6/1,613,582 alleles · ultra-rare
exomes 6/1,461,210 · genomes 0/152,372 · joint denominator
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
- KIF2A
- Protein
- p.Pro609=
- Coding
- c.1827A>G
- MANE Select
- NM_001098511
- dbSNP
- rs750351717
- Type
- single nucleotide variant
- Location
- chr5:62373753 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.76 (gnomAD)
- Structure
- AlphaFold pLDDT 79.37 · 6 PDB
Similar variants
- KIF2A p.Pro609Ser Uncertain significance ★ ⚠ same residue
- KIF2A p.Glu73Lys Likely pathogenic ★★ ⚠ same type
- KIF2A p.Gly313Glu Likely pathogenic ★★ same type
- KIF2A p.Ser317Asn Pathogenic ★★ same type
- KIF2A p.Thr320Ile Pathogenic/Likely pathogenic ★★ same type
- KIF2A p.Ala144Thr Uncertain significance ★★ ⚠ same type
- KIF2A p.Arg117His Uncertain significance ★★ ⚠ same type
- KIF2A p.Arg154His 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/kif2a-p-pro609 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown