CHAMP1 p.Pro105=
c.315T>A · rs144710092 · VCV3039812
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0483%, amr)
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 1.5 | GERP -0.55, phastCons 0.89 |
| Overall | ||
| CADD | 9.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0483%
Admixed American · 29/60,008 alleles
Filtering AF
0.0423%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.041%
Overall
0.037%
597/1,614,158 alleles · ultra-rare
exomes 540/1,461,840 · genomes 57/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0483% | 2,069 |
| European (non-Finnish) | 0.0455% | 2,197 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,290 |
| African / African-American | 0.016% | 6,253 |
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.Pro105=
- Coding
- c.315T>A
- MANE Select
- NM_032436
- dbSNP
- rs144710092
- Type
- single nucleotide variant
- Location
- chr13:114324157 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 48.04 · 4 PDB
- Residue 105
- the 'disordered' 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-pro105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown