KIF12 p.Pro485=
c.1455G>A · rs150940732 · VCV2907514
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.318%, 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 -13 | GERP -4.2 |
| Overall | ||
| CADD | 0.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.318%
African / African-American · 236/74,276 alleles
Filtering AF
0.284%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.272%
Overall
0.0198%
311/1,570,376 alleles · rare
exomes 158/1,418,218 · genomes 153/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.318% | 315 |
| South Asian | 0.0306% | 3,272 |
| Admixed American | 0.0302% | 3,314 |
| Remaining individualsnot grpmax-eligible | 0.0213% | 4,686 |
| Middle Eastern | 0.0167% | 5,990 |
| Finnishnot grpmax-eligible | 0.00163% | 61,256 |
| European (non-Finnish) | 0.00156% | 64,301 |
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
- KIF12
- Protein
- p.Pro485=
- Coding
- c.1455G>A
- MANE Select
- NM_001388308
- dbSNP
- rs150940732
- Type
- single nucleotide variant
- Location
- chr9:114093443 (GRCh38)
- Gene constraint
- LOEUF 1.106 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.01
- Residue 485
- a UniProt-annotated variant site (in pfic8); a UniProt-annotated variant site (found in a patient with liver cirrhosis; likely pathogenic; the orthologous mutation in a knockin mouse model results in features of liver steatosis with elevated liver triacylglycerol levels)
Similar variants
- KIF12 p.Pro485Leu Uncertain significance ★ ⚠ same residue
- KIF12 p.Arg293Ter Pathogenic ★★ same type
- KIF12 p.Val342Met Likely pathogenic ★★ same type
- KIF12 p.Ala417Thr Uncertain significance ★★ ⚠ same type
- KIF12 p.Arg333His Uncertain significance ★★ ⚠ same type
- KIF12 p.Arg468His Uncertain significance ★★ ⚠ same type
- KIF12 p.Gly609Arg Uncertain significance ★★ ⚠ same type
- KIF12 p.Leu356Val 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/kif12-p-pro485 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown