CHD9 p.Ser442=
c.1326G>A · rs747733475 · VCV2646531
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.2 | GERP -3.9 |
| Overall | ||
| CADD | 6.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,880 alleles
Filtering AF
0.00884%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.00112%
18/1,613,908 alleles · ultra-rare
exomes 13/1,461,698 · genomes 5/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,610 |
| African / African-American | 0.00533% | 18,752 |
| South Asian | 0.0022% | 45,539 |
| European (non-Finnish) | 0.000339% | 294,967 |
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
- CHD9
- Protein
- p.Ser442=
- Coding
- c.1326G>A
- MANE Select
- NM_001308319
- dbSNP
- rs747733475
- Type
- single nucleotide variant
- Location
- chr16:53157415 (GRCh38)
- Gene constraint
- LOEUF 0.309 · pLI 1.00 (gnomAD)
Similar variants
- CHD9 p.Ser442Leu Uncertain significance ★ ⚠ same residue
- CHD9 c.6620-2A>C Uncertain significance ★ same type
- CHD9 p.Ala1363Thr Uncertain significance ★ ⚠ same type
- CHD9 p.Ala1408Val Uncertain significance ★ ⚠ same type
- CHD9 p.Ala1537Thr Uncertain significance ★ same type
- CHD9 p.Ala167Val Uncertain significance ★ same type
- CHD9 p.Ala1724Gly Uncertain significance ★ same type
- CHD9 p.Ala1742Val 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/chd9-p-ser442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown