POP1 p.Lys299fs
c.897del · VCV3645545
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-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.91 | GERP -4, phastCons 0.98 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- POP1
- Protein
- p.Lys299fs
- Coding
- c.897del
- MANE Select
- NM_001145860
- Type
- Deletion
- Location
- chr8:98134543 (GRCh38)
- Structure
- AlphaFold pLDDT 76.08
Similar variants
- BVES p.Ser299Thr Uncertain significance ★ ⚠ same residue
- POPDC1 p.Ser299Phe Uncertain significance ★ ⚠ same residue
- BVES p.Phe244fs Likely pathogenic ★ same type
- POP1 p.Asp511fs Pathogenic ★ same type
- POP1 p.Gly506fs Pathogenic ★ same type
- POP1 p.Ile272fs Pathogenic ★ same type
- POP1 p.Ser116fs Pathogenic ★ same type
- POP1 p.Thr752fs 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/pop1-p-lys299fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown