CENPF p.Arg3003=
c.9007C>A · rs767547548 · VCV1336496
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, 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 0.58 | GERP 2.1, phastCons 0.19 |
| Overall | ||
| CADD | 8.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,900 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00062%
10/1,613,958 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,322 |
| European (non-Finnish) | 8.47e-05% | 1,179,988 |
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.Arg3003=
- Coding
- c.9007C>A
- MANE Select
- NM_016343
- dbSNP
- rs767547548
- Type
- single nucleotide variant
- Location
- chr1:214658894 (GRCh38)
- Gene constraint
- LOEUF 0.734 · pLI <0.01 (gnomAD)
- Residue 3003
- the 'sufficient for centromere localization' region; the 'sufficient for nuclear localization' region
Similar variants
- CENPF p.Arg3003Gln 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-arg3003 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown