KIF2A p.Val641=
c.1923C>A · rs1381133388 · VCV2917201
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00199%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.305 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 4.901 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00199%
Admixed American · 1/50,346 alleles
Filtering AF
0.00013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.5e-05%
Overall
0.000395%
6/1,520,220 alleles · very rare
exomes 6/1,367,934 · genomes 0/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00199% | 50,346 |
| European (non-Finnish) | 0.000445% | 224,837 |
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.Val641=
- Coding
- c.1923C>A
- MANE Select
- NM_001098511
- dbSNP
- rs1381133388
- Type
- single nucleotide variant
- Location
- chr5:62377672 (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-val641 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown