CENPE p.Pro121=
c.363T>G · rs139297376 · VCV739317
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.147%, 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 0.87 | GERP -2.5, phastCons 0.98 |
| Overall | ||
| CADD | 8.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
African / African-American · 106/72,324 alleles
Filtering AF
0.124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.115%
Overall
0.00789%
124/1,571,462 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.147% | 682 |
| Admixed American | 0.0169% | 5,908 |
| Remaining individualsnot grpmax-eligible | 0.0116% | 8,657 |
| European (non-Finnish) | 0.000257% | 388,831 |
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.Pro121=
- Coding
- c.363T>G
- MANE Select
- NM_001813
- dbSNP
- rs139297376
- Type
- single nucleotide variant
- Location
- chr4:103195228 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 (gnomAD)
- Residue 121
- the kinesin motor domain
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-pro121 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown