CHD2 p.Arg1644fs
c.4932_4935del · VCV3337250
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 38 of 39 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP 0.36, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CHD2
- Protein
- p.Arg1644fs
- Coding
- c.4932_4935del
- MANE Select
- NM_001271
- Type
- Microsatellite
- Location
- chr15:93020032 (GRCh38)
- Gene constraint
- LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.81
- Residue 1644
- 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.Arg1644Ser Uncertain significance ★★ ⚠ same residue
- CHD2 p.Arg1644Lys Uncertain significance ★ ⚠ same residue
- CHD2 p.Asp1107_Ser1108insTer Pathogenic ★★ same type
- CHD2 p.Glu1006_Asn1007insTer Pathogenic/Likely pathogenic ★★ same type
- CHD2 p.Glu551fs Pathogenic ★★ same type
- CHD2 p.Glu924del Likely pathogenic ★★ same type
- CHD2 p.Leu1591fs Pathogenic ★★ same type
- CHD2 p.Leu633fs 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-arg1644fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown