NPC2 p.Ile97fs
c.289del · VCV3383995
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Niemann-Pick disease
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 3 of 5 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NPC2
- Protein
- p.Ile97fs
- Coding
- c.289del
- MANE Select
- NM_006432
- Type
- Deletion
- Location
- chr14:74484489 (GRCh38)
- Gene constraint
- LOEUF 1.422 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.88 · 2 PDB
Similar variants
- NPC2 c.191-1_193del Likely pathogenic ★ same type
- NPC2 p.Ala5fs Pathogenic ★ same type
- NPC2 p.Asn111fs Pathogenic ★ same type
- NPC2 p.Asp31fs Likely pathogenic ★ same type
- NPC2 p.Ser50fs Likely pathogenic ★ same type
- NPC2 p.Thr44fs Pathogenic ★ same type
- NPC2 p.Thr62fs Likely pathogenic ★ same type
- NPC2 p.Tyr109fs Likely 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/npc2-p-ile97fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown