CENPI p.Ser149=
c.447C>T · rs201645922 · VCV2661051
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.161%, 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 0.1 | GERP 0.099, phastCons 0.93 |
| Overall | ||
| CADD | 8.258 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.161%
Middle Eastern · 7/4,339 alleles
Filtering AF
0.0757%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0537%
Overall
0.00389%
47/1,206,829 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.161% | 620 |
| South Asian | 0.0546% | 1,831 |
| Remaining individualsnot grpmax-eligible | 0.00632% | 15,833 |
| European (non-Finnish) | 0.000673% | 148,671 |
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
- CENPI
- Protein
- p.Ser149=
- Coding
- c.447C>T
- MANE Select
- NM_001386188
- dbSNP
- rs201645922
- Type
- single nucleotide variant
- Location
- chrX:101109555 (GRCh38)
- Structure
- AlphaFold pLDDT 74.27 · 12 PDB
- Residue 149
- an α-helix
Similar variants
- CENPI p.Val10Ile Benign ★★ same type
- CENPI p.Val276Met Benign ★★ same type
- CENPI c.1195+6A>G Uncertain significance ★ same type
- CENPI c.687+8C>T Uncertain significance ★ same type
- CENPI p.Ala147Gly Uncertain significance ★ ⚠ same type
- CENPI p.Ala479Val Uncertain significance ★ same type
- CENPI p.Ala674Asp Uncertain significance ★ ⚠ same type
- CENPI p.Ala692Thr 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/cenpi-p-ser149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown