CHD3 p.Ser1364=
c.4092G>A · rs118079592 · VCV3042191
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 9.44%, sas) — too common for a highly-penetrant pathogenic allele
Conditions
1
CHD3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.7 | GERP -3.8 |
| Overall | ||
| CADD | 1.571 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.44%
South Asian · 8,597/91,064 alleles
Filtering AF
9.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.21%
Overall
0.704%
11,371/1,614,154 alleles · common
exomes 10,640/1,461,862 · genomes 731/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 9.44% | 11 |
| East Asian | 1.64% | 61 |
| Middle Eastern | 1.12% | 89 |
| Remaining individualsnot grpmax-eligible | 1.11% | 90 |
| Ashkenazi Jewishnot grpmax-eligible | 0.541% | 185 |
| African / African-American | 0.14% | 715 |
| Admixed American | 0.113% | 883 |
| European (non-Finnish) | 0.0782% | 1,278 |
| Finnishnot grpmax-eligible | 0.0265% | 3,767 |
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.Ser1364=
- Coding
- c.4092G>A
- MANE Select
- NM_001005273
- dbSNP
- rs118079592
- Type
- single nucleotide variant
- Location
- chr17:7905119 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1364
- the 'disordered' region; a UniProt-annotated variant site (in snibcps)
Disease context
CHD3-related disorder
Similar variants
- CHD3 p.Ser1364Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1342Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg985Gln Pathogenic ★★ same condition
- CHD3 p.Arg1491His Uncertain significance ★★ ⚠ same condition
- CHD3 p.Arg684Ter Pathogenic ★ same condition
- CHD3 p.Glu1653Ter Likely pathogenic ★ same condition
- CHD3 p.Met1085Ile Likely pathogenic ★ 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/chd3-p-ser1364 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown