CHD1 p.Glu575=
c.1725A>G · rs146779749 · VCV3042175
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0655%, nfe)
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 0.27 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 6.829 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0655%
European (non-Finnish) · 705/1,075,580 alleles
Filtering AF
0.0615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0599%
Overall
0.0516%
763/1,477,972 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0655% | 1,526 |
| Remaining individualsnot grpmax-eligible | 0.054% | 1,851 |
| Middle Eastern | 0.0367% | 2,724 |
| Admixed American | 0.0189% | 5,298 |
| African / African-American | 0.0127% | 7,884 |
| Finnishnot grpmax-eligible | 0.00803% | 12,460 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00362% | 27,640 |
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
- CHD1
- Protein
- p.Glu575=
- Coding
- c.1725A>G
- MANE Select
- NM_001270
- dbSNP
- rs146779749
- Type
- single nucleotide variant
- Location
- chr5:98894672 (GRCh38)
- Gene constraint
- LOEUF 0.207 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.63 · 18 PDB
- Residue 575
- 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-glu575 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown