CHAMP1 p.Pro225=
c.675C>A · rs201875013 · VCV756072
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, sas)
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 -1.6 | GERP -1.2 |
| Overall | ||
| CADD | 4.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
South Asian · 1,141/91,080 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.17%
Overall
0.0851%
1,374/1,614,188 alleles · low-frequency
exomes 1,307/1,461,884 · genomes 67/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.25% | 80 |
| Middle Eastern | 0.214% | 466 |
| Remaining individualsnot grpmax-eligible | 0.0848% | 1,179 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,974 |
| European (non-Finnish) | 0.0126% | 7,920 |
| African / African-American | 0.00267% | 37,521 |
| East Asian | 0.00223% | 44,882 |
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
- CHAMP1
- Protein
- p.Pro225=
- Coding
- c.675C>A
- MANE Select
- NM_032436
- dbSNP
- rs201875013
- Type
- single nucleotide variant
- Location
- chr13:114324517 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 48.04 · 4 PDB
- Residue 225
- the 'disordered' region
Similar variants
- CHAMP1 p.Pro225Ser Uncertain significance ★ ⚠ same residue
- CHAMP1 p.Arg398Ter Pathogenic ★★ same type
- CHAMP1 p.Arg497Ter Pathogenic ★★ same type
- CHAMP1 p.Lys620Ter Pathogenic ★★ same type
- CHAMP1 p.Tyr709Ter Pathogenic/Likely pathogenic ★★ same type
- CHAMP1 p.Ala304Val Uncertain significance ★★ ⚠ same type
- CHAMP1 p.Glu195Gly Uncertain significance ★★ ⚠ same type
- CHAMP1 p.Glu524Gly 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/champ1-p-pro225 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown