CENPE p.Val52=
c.156C>G · VCV4821715
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0659%, mid)
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 2.1 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 8.945 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0659%
Middle Eastern · 4/6,072 alleles
Filtering AF
0.037%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.033%
Overall
0.00516%
83/1,606,970 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0659% | 1,518 |
| South Asian | 0.0484% | 2,066 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,573 |
| Admixed American | 0.00334% | 29,972 |
| European (non-Finnish) | 0.00247% | 40,530 |
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.Val52=
- Coding
- c.156C>G
- MANE Select
- NM_001813
- Type
- single nucleotide variant
- Location
- chr4:103196245 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 (gnomAD)
- Residue 52
- the kinesin motor domain; a β-strand
Similar variants
- 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
- CENPE p.Gln2022Glu 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-val52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown