CLPX p.Ile429=
c.1287C>A · VCV4767738
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 2.7 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 7.827 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,150 alleles
Overall
6.85e-05%
1/1,459,950 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
- CLPX
- Protein
- p.Ile429=
- Coding
- c.1287C>A
- MANE Select
- NM_006660
- Type
- single nucleotide variant
- Location
- chr15:65155716 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 67.22 · 3 PDB
Similar variants
- 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
- CLPX p.Glu614Gly 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-ile429 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown