CENPF p.Lys2785=
c.8355G>A · VCV3704534
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0202%, 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 3.5 | GERP 0.38, phastCons 1 |
| Overall | ||
| CADD | 7.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0202%
East Asian · 9/44,540 alleles
Filtering AF
0.0105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00784%
Overall
0.000619%
9/1,452,888 alleles · ultra-rare
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.Lys2785=
- Coding
- c.8355G>A
- MANE Select
- NM_016343
- Type
- single nucleotide variant
- Location
- chr1:214655273 (GRCh38)
- Gene constraint
- LOEUF 0.734 · pLI <0.01 (gnomAD)
- Residue 2785
- the 'sufficient for centromere localization' region; the 'sufficient for self-association' region
Similar variants
- 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
- CENPF p.Glu361Ter Likely 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-lys2785 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown