CHAMP1 p.Pro561=
c.1683T>C · rs144530612 · VCV728493
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0144%, nfe)
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 -0.8 | GERP 0.54, phastCons 0.016 |
| Overall | ||
| CADD | 3.941 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0144%
European (non-Finnish) · 170/1,180,046 alleles
Filtering AF
0.0126%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0119%
Overall
0.0108%
175/1,614,054 alleles · ultra-rare
exomes 169/1,461,876 · genomes 6/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0144% | 6,941 |
| Finnishnot grpmax-eligible | 0.00469% | 21,341 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
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.Pro561=
- Coding
- c.1683T>C
- MANE Select
- NM_032436
- dbSNP
- rs144530612
- Type
- single nucleotide variant
- Location
- chr13:114325525 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 48.04 · 4 PDB
- Residue 561
- the 'mediates localization to the spindle and the kinetochore and is required for the attachment of spindle microtubules to the kinetochore' region
Similar variants
- 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
- CHAMP1 p.Glu668Gln 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-pro561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown