KIF12 p.Pro375=
c.1125T>C · rs755506925 · VCV2823058
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 | GERP -3.8 |
| Overall | ||
| CADD | 2.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- KIF12
- Protein
- p.Pro375=
- Coding
- c.1125T>C
- MANE Select
- NM_001388308
- dbSNP
- rs755506925
- Type
- single nucleotide variant
- Location
- chr9:114094450 (GRCh38)
- Gene constraint
- LOEUF 1.106 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.01
- Residue 375
- 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.Pro375Ser 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-pro375 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown