KIF15 p.Phe86=
c.258C>T · rs745815466 · VCV3114480
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 1.7 | GERP 0.82, phastCons 1 |
| Overall | ||
| CADD | 13.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,872 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000868%
14/1,612,860 alleles · very rare
exomes 10/1,460,762 · genomes 4/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,479 |
| East Asian | 0.00446% | 22,433 |
| South Asian | 0.00329% | 30,357 |
| Admixed American | 0.00167% | 59,980 |
| European (non-Finnish) | 0.00017% | 589,501 |
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
- KIF15
- Protein
- p.Phe86=
- Coding
- c.258C>T
- MANE Select
- NM_020242
- dbSNP
- rs745815466
- Type
- single nucleotide variant
- Location
- chr3:44778126 (GRCh38)
- Gene constraint
- LOEUF 0.891 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.23 · 4 PDB
- Residue 86
- the kinesin motor domain; an α-helix
Similar variants
- KIF15 p.Leu844Val Uncertain significance ★★ ⚠ same type
- KIF15 p.Val239Ile Uncertain significance ★★ ⚠ same type
- KIF15 c.2550-6A>G Benign ★★ same type
- KIF15 c.3049-7T>C Benign ★★ same type
- KIF15 p.Ala1375= Benign/Likely benign ★★ same type
- KIF15 p.Ala211Val Likely benign ★★ same type
- KIF15 p.Ala392= Benign ★★ same type
- KIF15 p.Asn495Asp Benign ★★ 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/kif15-p-phe86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown