NF1 p.Phe960fs
c.2877dup · VCV4293366
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
neurofibromatosis type 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 22 of 58 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.1, phastCons 1 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NF1
- Protein
- p.Phe960fs
- Coding
- c.2877dup
- MANE Select
- NM_001042492
- Type
- Duplication
- Location
- chr17:31229859 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 960
- an α-helix
Disease context
neurofibromatosis type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Neurofibromatosis type 1 (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Infancy, Neonatal
- Prevalence
- 1-5 / 10 000 (United Kingdom)
Similar variants
- NF1 p.Phe960= Conflicting classifications of pathogenicity ★ same residue
- NF1 c.654+2dup Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.7970+2dup Likely pathogenic ★★ same condition
- NF1 p.Ala1530fs Pathogenic ★★ same condition
- NF1 p.Ala219fs Pathogenic ★★ same condition
- NF1 p.Ala264fs Pathogenic ★★ same condition
- NF1 p.Ala671fs Pathogenic ★★ same condition
- NF1 p.Arg2119fs Pathogenic/Likely 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/nf1-p-phe960fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown