CHD2 p.Tyr487fs
c.1459del · rs2141802547 · VCV1319260
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 13 of 39 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CHD2
- Protein
- p.Tyr487fs
- Coding
- c.1459del
- MANE Select
- NM_001271
- dbSNP
- rs2141802547
- Type
- Deletion
- Location
- chr15:92949032 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
- Residue 487
- a UniProt-annotated variant site (in dee94); a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy; uncertain significance)
Similar variants
- CHD2 p.Glu1412fs Pathogenic ★★ same type
- CHD2 p.Lys1393fs Pathogenic ★★ same type
- CHD2 p.Lys174_Val175insTer Pathogenic/Likely pathogenic ★★ same type
- CHD2 p.Pro399fs Pathogenic ★★ same type
- CHD2 c.1199-12del Benign/Likely benign ★★ same type
- CHD2 c.381+12del Likely benign ★★ same type
- CHD2 p.Lys1411del Benign/Likely benign ★★ same type
- CHD2 c.1151_1153+4del Likely pathogenic ★ 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/chd2-p-tyr487fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown