CENPE p.Leu644=
c.1932T>C · rs1754427890 · VCV2654987
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.85e-05%)
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 0.68 | GERP -2.3, phastCons 0.94 |
| Overall | ||
| CADD | 6.053 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.85e-05%
Overall
6.85e-05%
1/1,459,754 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.Leu644=
- Coding
- c.1932T>C
- MANE Select
- NM_001813
- dbSNP
- rs1754427890
- Type
- single nucleotide variant
- Location
- chr4:103161368 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 (gnomAD)
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-leu644 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown