KIF14 p.Pro680=
c.2040C>T · rs147146959 · VCV2443156
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.113%, 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 -5 | GERP -3.8 |
| Overall | ||
| CADD | 3.096 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.113%
African / African-American · 85/75,006 alleles
Filtering AF
0.0938%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0867%
Overall
0.00892%
144/1,613,734 alleles · rare
exomes 100/1,461,512 · genomes 44/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.113% | 882 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,975 |
| Middle Eastern | 0.033% | 3,028 |
| South Asian | 0.0154% | 6,502 |
| Admixed American | 0.0117% | 8,570 |
| East Asian | 0.00223% | 44,834 |
| European (non-Finnish) | 0.00119% | 84,275 |
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
- KIF14
- Protein
- p.Pro680=
- Coding
- c.2040C>T
- MANE Select
- NM_014875
- dbSNP
- rs147146959
- Type
- single nucleotide variant
- Location
- chr1:200602008 (GRCh38)
- Gene constraint
- LOEUF 0.65 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.68
- Residue 680
- the kinesin motor domain; a UniProt-annotated variant site (in mcph20; drastically decreased expression at the mrna level; loss of localization at the midbody during cytokinesis and consequently loss of cit/crik recruitment to the midbody); the 'required for microtubule-binding with high affinity' region
Similar variants
- KIF14 c.3661+1G>T Likely pathogenic ★★ same type
- KIF14 p.Arg35Ter Pathogenic/Likely pathogenic ★★ same type
- KIF14 c.3114+3A>C Uncertain significance ★★ same type
- KIF14 p.Ala605Ser Uncertain significance ★★ ⚠ same type
- KIF14 p.Ala776Asp Uncertain significance ★★ ⚠ same type
- KIF14 p.Arg1624His Uncertain significance ★★ ⚠ same type
- KIF14 p.Arg609His Uncertain significance ★★ ⚠ same type
- KIF14 p.Arg699Cys 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/kif14-p-pro680 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown