CENPF p.Ala466=
c.1398G>A · rs139822426 · VCV712345
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.86%, eas)
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 -4.9 | GERP -4.9 |
| Overall | ||
| CADD | 3.489 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.86%
East Asian · 386/44,862 alleles
Filtering AF
0.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.762%
Overall
0.0323%
521/1,614,080 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.86% | 116 |
| Remaining individualsnot grpmax-eligible | 0.128% | 781 |
| African / African-American | 0.0173% | 5,773 |
| South Asian | 0.0121% | 8,280 |
| Admixed American | 0.005% | 20,006 |
| European (non-Finnish) | 0.00237% | 42,142 |
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
- CENPF
- Protein
- p.Ala466=
- Coding
- c.1398G>A
- MANE Select
- NM_016343
- dbSNP
- rs139822426
- Type
- single nucleotide variant
- Location
- chr1:214632554 (GRCh38)
- Gene constraint
- LOEUF 0.734 · pLI <0.01 (gnomAD)
- Residue 466
- the 'interaction with snap25 and required for localization to the cytoplasm' region
Similar variants
- CENPF p.Ala466Val Uncertain significance ★ ⚠ same residue
- CENPF c.1195-2A>G Likely pathogenic ★★ same type
- CENPF c.1323+1G>A Pathogenic ★★ same type
- CENPF p.Arg1667Ter Pathogenic/Likely pathogenic ★★ same type
- CENPF p.Arg2407Ter Pathogenic/Likely pathogenic ★★ same type
- CENPF p.Arg2898Ter Pathogenic ★★ same type
- CENPF p.Arg3094Ter Likely pathogenic ★★ same type
- CENPF p.Glu1257Ter Pathogenic ★★ 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/cenpf-p-ala466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown