CHERP p.Pro539=
c.1617G>A · rs201185399 · VCV2649512
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.215%, afr)
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 -9 | GERP -3.7 |
| Overall | ||
| CADD | 1.024 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.215%
African / African-American · 152/70,640 alleles
Filtering AF
0.187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.177%
Overall
0.0118%
176/1,491,886 alleles · rare
exomes 89/1,339,616 · genomes 87/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.215% | 465 |
| Middle Eastern | 0.0179% | 5,576 |
| Remaining individualsnot grpmax-eligible | 0.00873% | 11,456 |
| Admixed American | 0.00476% | 21,016 |
| European (non-Finnish) | 0.00143% | 70,061 |
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
- CHERP
- Protein
- p.Pro539=
- Coding
- c.1617G>A
- MANE Select
- NM_006387
- dbSNP
- rs201185399
- Type
- single nucleotide variant
- Location
- chr19:16525366 (GRCh38)
- Gene constraint
- LOEUF 0.152 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.55
- Residue 539
- the 'disordered' region
Similar variants
- CHERP p.Ala125Glu Uncertain significance ★ ⚠ same type
- CHERP p.Ala125Thr Uncertain significance ★ ⚠ same type
- CHERP p.Ala125Val Uncertain significance ★ ⚠ same type
- CHERP p.Ala175Val Uncertain significance ★ ⚠ same type
- CHERP p.Ala367Asp Uncertain significance ★ ⚠ same type
- CHERP p.Ala403Gly Uncertain significance ★ ⚠ same type
- CHERP p.Ala61Val Uncertain significance ★ ⚠ same type
- CHERP p.Ala93Thr 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/cherp-p-pro539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown