CENPE p.Ile2152=
c.6456T>C · rs765456583 · VCV763489
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 1.1 | GERP -3.7, phastCons 0.99 |
| Overall | ||
| CADD | 4.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,018 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000205%
3/1,461,586 alleles · very 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
- CENPE
- Protein
- p.Ile2152=
- Coding
- c.6456T>C
- MANE Select
- NM_001813
- dbSNP
- rs765456583
- Type
- single nucleotide variant
- Location
- chr4:103136207 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 (gnomAD)
- Residue 2152
- the 'kinetochore-binding domain' region
Similar variants
- CENPE p.Ile2152Thr Uncertain significance ★ ⚠ same residue
- CENPE p.Arg2279Cys Uncertain significance ★★ ⚠ same type
- CENPE p.Arg760Ser Uncertain significance ★★ ⚠ same type
- CENPE p.Asn1145Lys Uncertain significance ★★ ⚠ same type
- CENPE p.Asn1165Ser Uncertain significance ★★ ⚠ same type
- CENPE p.Asp1960Tyr Uncertain significance ★★ ⚠ same type
- CENPE p.Asp954Asn Uncertain significance ★★ same type
- CENPE p.Asp954Tyr 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/cenpe-p-ile2152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown