CHD3 p.Ala241fs
c.720del · VCV3383503
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 40 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.00928% | 10,778 |
| African / African-Americangrpmax | 0.00307% | 32,534 |
| European (non-Finnish) | 0.00278% | 36,036 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- CHD3
- Protein
- p.Ala241fs
- Coding
- c.720del
- MANE Select
- NM_001005273
- Type
- Deletion
- Location
- chr17:7893491 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 241
- the 'disordered' region
Similar variants
- CHD3 p.Ala241Thr Likely benign ★ same residue
- CHD3 p.Pro88_Pro92del Likely benign ★★ same type
- CHD3 p.Ala1127fs Pathogenic ★ same type
- CHD3 p.Ala191fs Likely pathogenic ★ same type
- CHD3 p.Arg1381fs Likely pathogenic ★ same type
- CHD3 p.Glu1362fs Pathogenic ★ same type
- CHD3 p.Glu519fs Likely pathogenic ★ same type
- CHD3 p.Lys1044fs Likely pathogenic ★ 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/chd3-p-ala241fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown