KIF5C p.Pro46=
c.138A>G · rs560119808 · VCV1246884
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.68%, sas)
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 -3.1 | GERP -2.9 |
| Overall | ||
| CADD | 5.798 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.68%
South Asian · 1,505/89,798 alleles
Filtering AF
1.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.58%
Overall
0.0989%
1,591/1,607,922 alleles · low-frequency
exomes 1,517/1,455,608 · genomes 74/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.68% | 60 |
| Middle Eastern | 0.182% | 549 |
| Remaining individualsnot grpmax-eligible | 0.0594% | 1,683 |
| Admixed American | 0.00679% | 14,726 |
| European (non-Finnish) | 0.0028% | 35,668 |
| African / African-American | 0.00134% | 74,788 |
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.Pro46=
- Coding
- c.138A>G
- MANE Select
- NM_004522
- dbSNP
- rs560119808
- Type
- single nucleotide variant
- Location
- chr2:148922148 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.70
- Residue 46
- the kinesin motor domain
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-pro46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown