CHD1 p.Lys600=
c.1800G>A · VCV3769608
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Hypotonia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.77 | donor loss at this position · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.74 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 21.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CHD1
- Protein
- p.Lys600=
- Coding
- c.1800G>A
- MANE Select
- NM_001270
- Type
- single nucleotide variant
- Location
- chr5:98894597 (GRCh38)
- Gene constraint
- LOEUF 0.207 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.63 · 18 PDB
- Residue 600
- an α-helix; the helicase atp-binding domain
Similar variants
- CHD1 p.Arg1378Gly Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg1659Thr Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg1676Gly Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg1708Gln Uncertain significance ★★ same type
- CHD1 p.Arg1708Trp Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg233His Uncertain significance ★★ same type
- CHD1 p.Arg70Ter Uncertain significance ★★ same type
- CHD1 p.Asn1518His 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/chd1-p-lys600 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown