CLPX p.Ala24=
c.72G>A · rs759817379 · VCV2159269
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0227%, amr)
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 0.047 | GERP 0.091, phastCons 0.87 |
| Overall | ||
| CADD | 12.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0227%
Admixed American · 12/52,948 alleles
Filtering AF
0.013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0102%
Overall
0.00108%
17/1,572,932 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0227% | 4,412 |
| East Asian | 0.00466% | 21,476 |
| Remaining individualsnot grpmax-eligible | 0.00329% | 30,437 |
| European (non-Finnish) | 8.62e-05% | 1,160,056 |
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.Ala24=
- Coding
- c.72G>A
- MANE Select
- NM_006660
- dbSNP
- rs759817379
- Type
- single nucleotide variant
- Location
- chr15:65185082 (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-ala24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown