CLPX p.Arg15=
c.45G>A · rs374002701 · VCV1977713
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00146%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.023 | GERP -1.9, phastCons 0.89 |
| Overall | ||
| CADD | 5.793 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00146%
European (non-Finnish) · 17/1,166,032 alleles
Filtering AF
0.000888%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000726%
Overall
0.00107%
17/1,583,598 alleles · very rare
exomes 16/1,431,656 · genomes 1/151,942 · joint denominator
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.Arg15=
- Coding
- c.45G>A
- MANE Select
- NM_006660
- dbSNP
- rs374002701
- Type
- single nucleotide variant
- Location
- chr15:65185109 (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-arg15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown