CLPX p.Arg565=
c.1695G>T · rs145963384 · VCV1599106
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.391%, 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 -0.98 | GERP -3.7, phastCons 0.002 |
| Overall | ||
| CADD | 6.962 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.391%
African / African-American · 289/73,884 alleles
Filtering AF
0.354%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.34%
Overall
0.0201%
320/1,589,536 alleles · rare
exomes 163/1,437,262 · genomes 157/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.391% | 256 |
| Middle Eastern | 0.05% | 2,002 |
| Remaining individualsnot grpmax-eligible | 0.0275% | 3,630 |
| Admixed American | 0.0123% | 8,099 |
| European (non-Finnish) | 0.000343% | 291,244 |
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.Arg565=
- Coding
- c.1695G>T
- MANE Select
- NM_006660
- dbSNP
- rs145963384
- Type
- single nucleotide variant
- Location
- chr15:65153556 (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-arg565 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown