KIF2A p.Pro643=
c.1929A>G · rs201710140 · VCV780538
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.135%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.027 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 8.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.135%
African / African-American · 99/73,090 alleles
Filtering AF
0.114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.106%
Overall
0.00772%
119/1,542,106 alleles · rare
exomes 63/1,389,746 · genomes 56/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.135% | 738 |
| Admixed American | 0.027% | 3,698 |
| Remaining individualsnot grpmax-eligible | 0.0067% | 14,934 |
| European (non-Finnish) | 0.000176% | 568,974 |
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.Pro643=
- Coding
- c.1929A>G
- MANE Select
- NM_001098511
- dbSNP
- rs201710140
- Type
- single nucleotide variant
- Location
- chr5:62377678 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.76 (gnomAD)
- Structure
- AlphaFold pLDDT 79.37 · 6 PDB
Similar variants
- 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
- KIF2A p.Arg402Trp 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-pro643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown