NIPBL p.Phe2409fs
c.7227_7230del · VCV3642666
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Cornelia de Lange syndrome 1
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 haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 42 of 47 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NIPBL
- Protein
- p.Phe2409fs
- Coding
- c.7227_7230del
- MANE Select
- NM_133433
- Type
- Deletion
- Location
- chr5:37052527 (GRCh38)
- Gene constraint
- LOEUF 0.057 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- NIPBL p.Asn1897del Pathogenic/Likely pathogenic ★★ same condition
- NIPBL p.Leu2597fs Pathogenic ★★ same condition
- NIPBL p.Lys2767fs Pathogenic/Likely pathogenic ★★ same condition
- NIPBL p.Lys603fs Pathogenic/Likely pathogenic ★★ same condition
- NIPBL p.Pro29fs Pathogenic ★★ same condition
- NIPBL p.Pro736fs Pathogenic ★★ same condition
- NIPBL p.Ser1797fs Pathogenic ★★ same condition
- NIPBL p.Val2227fs Pathogenic ★★ 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/nipbl-p-phe2409fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown