CLPX p.Ser466=
c.1398G>A · rs35370045 · VCV1603579
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.109%, 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 -0.14 | GERP -0.33, phastCons 0.7 |
| Overall | ||
| CADD | 8.475 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.109%
African / African-American · 82/75,008 alleles
Filtering AF
0.0902%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0832%
Overall
0.00576%
93/1,614,062 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.109% | 915 |
| Middle Eastern | 0.0165% | 6,060 |
| Admixed American | 0.00333% | 29,998 |
| East Asian | 0.00223% | 44,876 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
| European (non-Finnish) | 0.000508% | 196,667 |
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
- CLPX
- Protein
- p.Ser466=
- Coding
- c.1398G>A
- MANE Select
- NM_006660
- dbSNP
- rs35370045
- Type
- single nucleotide variant
- Location
- chr15:65154995 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 67.22 · 3 PDB
Similar variants
- CLPX p.Ser466Leu Uncertain significance ★ ⚠ same residue
- CLPX p.Ala13Val Uncertain significance ★★ ⚠ same type
- CLPX p.Ala65Ser Uncertain significance ★★ ⚠ same type
- CLPX p.Arg270Gln Uncertain significance ★★ ⚠ same type
- CLPX p.Asn424Ser Uncertain significance ★★ ⚠ same type
- CLPX p.Gln352His Uncertain significance ★★ ⚠ same type
- CLPX p.Gln47Arg Uncertain significance ★★ ⚠ same type
- CLPX p.Glu539Lys 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/clpx-p-ser466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown