CDT1 p.Arg469fs
c.1405dup · VCV3653953
Pathogenic
Single submitter
Classification
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 |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 10 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 0.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDT1
- Protein
- p.Arg469fs
- Coding
- c.1405dup
- MANE Select
- NM_030928
- Type
- Duplication
- Location
- chr16:88807409 (GRCh38)
- Gene constraint
- LOEUF 1.737 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.51 · 6 PDB
- Residue 469
- the 'interaction with lrwd1' region
Similar variants
- CDT1 p.Arg469His Uncertain significance ★★ ⚠ same residue
- CDT1 p.Arg469Cys Uncertain significance ★ ⚠ same residue
- CDT1 p.Arg19fs Pathogenic ★ same type
- CDT1 p.Glu504fs Pathogenic ★ same type
- CDT1 p.Ser391fs Pathogenic ★ same type
- CDT1 c.228+4_228+5dup Conflicting classifications of pathogenicity ★ same type
- CDT1 c.1477+13_1477+34dup Likely benign ★ 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/cdt1-p-arg469fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown