CHD3 p.Arg684Ter
c.2050C>T · VCV4933412
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
CHD3-related disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 40 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP 0.88, phastCons 1 |
| Overall | ||
| CADD | 40.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CHD3
- Protein
- p.Arg684Ter
- Coding
- c.2050C>T
- MANE Select
- NM_001005273
- Type
- single nucleotide variant
- Location
- chr17:7898101 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 684
- a UniProt-annotated variant site (in snibcps)
Disease context
CHD3-related disorders
Similar variants
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1342Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg985Gln Pathogenic ★★ same condition
- CHD3 p.Arg1491His Uncertain significance ★★ ⚠ same condition
- CHD3 p.Glu1653Ter Likely pathogenic ★ same condition
- CHD3 p.Met1085Ile Likely pathogenic ★ same condition
- CHD3 p.Ala1289Thr Conflicting classifications of pathogenicity ★ ⚠ same condition
- CHD3 p.Arg1342Trp Conflicting classifications of pathogenicity ★ ⚠ 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/chd3-p-arg684ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown