KDM5A p.Trp1466fs
c.4395dup · VCV3368463
Uncertain significance
Single submitter
Classification
Uncertain significance
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 LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 26 of 28 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- KDM5A
- Protein
- p.Trp1466fs
- Coding
- c.4395dup
- MANE Select
- NM_001042603
- Type
- Duplication
- Location
- chr12:295632 (GRCh38)
- Gene constraint
- LOEUF 0.27 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.98 · 46 PDB
- Residue 1466
- a UniProt-annotated variant site (found in a patient with severe intellectual disability, developmental delay, focal epilepsy, tetraspastic gait, ataxia and behavioral difficulties; uncertain significance)
Similar variants
- KDM5A p.Trp1466Arg Uncertain significance ★ ⚠ same residue
- KDM5A c.2151-14_2151-5dup Likely benign ★★ same type
- KDM5A c.2151-15_2151-5dup Likely benign ★★ same type
- KDM5A p.Tyr9fs Pathogenic ★ same type
- KDM5A c.2151-10_2151-5dup Likely benign ★ same type
- KDM5A c.2151-13_2151-5dup Likely benign ★ same type
- KDM5A c.2151-16_2151-5dup Likely benign ★ same type
- KDM5A c.2151-17_2151-5dup 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/kdm5a-p-trp1466fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown