CHD1L p.Ser441=
c.1323T>C · rs2275250 · VCV3050020
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.77%, eas)
Conditions
1
CHD1L-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -3.7 |
| Overall | ||
| CADD | 5.877 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.77%
East Asian · 1,242/44,872 alleles
Filtering AF
2.64%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.59%
Overall
0.128%
2,073/1,614,158 alleles · low-frequency
exomes 1,760/1,461,856 · genomes 313/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.77% | 36 |
| Ashkenazi Jewishnot grpmax-eligible | 0.537% | 186 |
| Remaining individualsnot grpmax-eligible | 0.216% | 463 |
| South Asian | 0.171% | 584 |
| Middle Eastern | 0.099% | 1,010 |
| Finnishnot grpmax-eligible | 0.0328% | 3,050 |
| European (non-Finnish) | 0.0291% | 3,440 |
| Admixed American | 0.015% | 6,669 |
| African / African-American | 0.00267% | 37,521 |
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
- CHD1L
- Protein
- p.Ser441=
- Coding
- c.1323T>C
- MANE Select
- NM_004284
- dbSNP
- rs2275250
- Type
- single nucleotide variant
- Location
- chr1:147275406 (GRCh38)
- Gene constraint
- LOEUF 1.152 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.81 · 7 PDB
- Residue 441
- the helicase c-terminal domain
Disease context
CHD1L-related disorder
Similar variants
- CHD1L p.Gln594Pro Uncertain significance ★★ same condition
- CHD1L p.Gln594His Uncertain significance ★ ⚠ same condition
- CHD1L p.Ser420Asn Uncertain significance ⚠ same condition
- CHD1L c.1386-2A>G Likely benign same condition
- CHD1L p.Arg37= Likely benign same condition
- CHD1L p.Arg663Lys Likely benign same condition
- CHD1L p.Gln549= Likely benign same condition
- CHD1L p.Leu57= Likely benign 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/chd1l-p-ser441 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown