CHAMP1 p.Val412=
c.1236T>C · VCV4920807
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 -0.071 | GERP -0.69, phastCons 0.54 |
| Overall | ||
| CADD | 4.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,880 alleles
Overall
0.000124%
2/1,613,982 alleles · very rare
exomes 2/1,461,894 · genomes 0/152,088 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,880 |
| European (non-Finnish) | 8.47e-05% | 1,179,997 |
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.Val412=
- Coding
- c.1236T>C
- MANE Select
- NM_032436
- Type
- single nucleotide variant
- Location
- chr13:114325078 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 48.04 · 4 PDB
- Residue 412
- the 'disordered' region; the 'mediates interaction with mad2l2' 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-val412 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown