KIF5C p.Phe209=
c.627C>T · VCV4956966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.123%, 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 4 | GERP 2.9, phastCons 1 |
| Overall | ||
| CADD | 13.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.123%
East Asian · 55/44,826 alleles
Filtering AF
0.0968%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0874%
Overall
0.0106%
171/1,613,078 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.123% | 815 |
| Middle Eastern | 0.0826% | 1,211 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,922 |
| South Asian | 0.0088% | 11,361 |
| European (non-Finnish) | 0.00805% | 12,418 |
| Finnishnot grpmax-eligible | 0.00156% | 63,960 |
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
- KIF5C
- Protein
- p.Phe209=
- Coding
- c.627C>T
- MANE Select
- NM_004522
- Type
- single nucleotide variant
- Location
- chr2:148946936 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.70
- Residue 209
- the kinesin motor domain; the 'microtubule-binding' region
Similar variants
- KIF5C p.Glu237Lys Pathogenic/Likely pathogenic ★★ same type
- KIF5C p.Lys92Arg Likely pathogenic ★★ same type
- KIF5C p.Thr93Ile Pathogenic/Likely pathogenic ★★ same type
- KIF5C p.Tyr135Cys Likely pathogenic ★★ same type
- KIF5C p.Arg286Trp Uncertain significance ★★ ⚠ same type
- KIF5C p.Arg927Cys Uncertain significance ★★ ⚠ same type
- KIF5C p.Met891Thr Uncertain significance ★★ same type
- KIF5C p.Pro932Leu 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/kif5c-p-phe209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown