KIF2A p.Asp65=
c.195C>T · VCV3662151
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.26 | phastCons 0.98 |
| Overall | ||
| CADD | 9.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,726 alleles
Overall
6.2e-05%
1/1,613,756 alleles · very rare
exomes 1/1,461,480 · genomes 0/152,276 · 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.Asp65=
- Coding
- c.195C>T
- MANE Select
- NM_001098511
- Type
- single nucleotide variant
- Location
- chr5:62348083 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.76 (gnomAD)
- Structure
- AlphaFold pLDDT 79.37 · 6 PDB
- Residue 65
- the 'globular' region
Similar variants
- KIF2A p.Asp65Glu Benign ★★ 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-asp65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown