CHAMP1 p.Pro172=
c.516T>A · rs189158463 · VCV728926
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.105%, eas)
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 | GERP -0.67, phastCons 1 |
| Overall | ||
| CADD | 6.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.105%
East Asian · 47/44,880 alleles
Filtering AF
0.0808%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0725%
Overall
0.00477%
77/1,614,128 alleles · rare
exomes 69/1,461,892 · genomes 8/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.105% | 955 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,232 |
| Admixed American | 0.00167% | 60,016 |
| South Asian | 0.0011% | 91,084 |
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.Pro172=
- Coding
- c.516T>A
- MANE Select
- NM_032436
- dbSNP
- rs189158463
- Type
- single nucleotide variant
- Location
- chr13:114324358 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 48.04 · 4 PDB
- Residue 172
- the 'disordered' region
Similar variants
- CHAMP1 p.Pro172Arg 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-pro172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown