CHD1 p.Lys431=
c.1293A>G · VCV3902447
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000255%, nfe)
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 2.4 | GERP 0.6, phastCons 1 |
| Overall | ||
| CADD | 9.949 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000255%
European (non-Finnish) · 3/1,174,904 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000187%
3/1,602,542 alleles · very rare
exomes 3/1,450,228 · genomes 0/152,314 · joint denominator
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.Lys431=
- Coding
- c.1293A>G
- MANE Select
- NM_001270
- Type
- single nucleotide variant
- Location
- chr5:98898328 (GRCh38)
- Gene constraint
- LOEUF 0.207 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.63 · 18 PDB
- Residue 431
- the chromo 2 domain; an α-helix
Similar variants
- CHD1 p.Lys431Arg Uncertain significance ★ ⚠ same residue
- 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
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-lys431 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown