CHD7 p.Lys643fs
c.1925dup · VCV3720827
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
2
CHARGE syndrome
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 haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 38 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.6, phastCons 1 |
| Region caveats | ||
| Repeat context | tandem | A-rich low complexity · ambiguous alignment · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CHD7
- Protein
- p.Lys643fs
- Coding
- c.1925dup
- MANE Select
- NM_017780
- Type
- Duplication
- Location
- chr8:60781252 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 643
- the 'disordered' region
Similar variants
- CHD7 p.Lys643Thr Uncertain significance ★ same residue
- CHD7 p.Asp2988fs Pathogenic/Likely pathogenic ★★ same condition
- CHD7 p.Asp652fs Pathogenic/Likely pathogenic ★★ same condition
- CHD7 p.Glu664fs Pathogenic ★★ same condition
- CHD7 p.Leu2916fs Pathogenic/Likely pathogenic ★★ same condition
- CHD7 p.Tyr2601fs Pathogenic/Likely pathogenic ★★ same condition
- CHD7 p.Tyr2601Ter Pathogenic ★★ same condition
- CHD7 p.Asn2818dup Uncertain significance ★★ same condition
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/chd7-p-lys643fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown