CHD6 p.Lys359=
c.1077G>A · rs950858253 · VCV2652336
Uncertain significance
Single submitter
Classification
Uncertain significance
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. | ||
| REVEL | 0.061 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.4 | phastCons 1 |
| Overall | ||
| CADD | 12.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,828 alleles
Overall
6.85e-05%
1/1,459,322 alleles · very rare
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
- CHD6
- Protein
- p.Lys359=
- Coding
- c.1077G>A
- MANE Select
- NM_032221
- dbSNP
- rs950858253
- Type
- single nucleotide variant
- Location
- chr20:41497399 (GRCh38)
- Gene constraint
- LOEUF 0.221 · pLI 1.00 (gnomAD)
- Residue 359
- the 'required for dna-dependent atpase activity' region
Similar variants
- CHD6 c.1858-19G>A Benign ★★ same type
- CHD6 c.554+5G>A Benign/Likely benign ★★ same type
- CHD6 c.852+4T>C Benign ★★ same type
- CHD6 p.Ala1205Gly Benign ★★ same type
- CHD6 p.Arg2389Cys Benign ★★ same type
- CHD6 p.Glu1271= Benign ★★ same type
- CHD6 p.Glu2404Gln Benign ★★ same type
- CHD6 p.Gly1519Asp Benign ★★ 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/chd6-p-lys359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown