Is NF2 p.Phe96del (c.285CTT[1]) pathogenic?

NF2 p.Phe96del (c.285CTT[1]) is classified Conflicting classifications of pathogenicity in NF2 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2024-11-14). Absent from gnomAD; Associated with NF2-related disorder.

What condition is associated with NF2 p.Phe96del (c.285CTT[1])?

NF2 p.Phe96del (c.285CTT[1]) is associated with NF2-related disorder, NF2-related schwannomatosis, hereditary neoplastic syndrome (ClinVar).

How common is NF2 p.Phe96del (c.285CTT[1]) in the general population?

NF2 p.Phe96del (c.285CTT[1]) is absent from gnomAD (gnomAD).

NF2 p.Phe96del

c.285CTT[1] · rs121434260 · VCV3288

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

NF2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.2	GERP 1.3, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: NF2
Protein: p.Phe96del
Coding: c.285CTT[1]
MANE Select: NM_000268
dbSNP: rs121434260
Type: Microsatellite
Location: chr22:29639134 (GRCh38)
Gene constraint: LOEUF 0.187 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 87.85 · 6 PDB
Residue 96: the ferm domain; a UniProt-annotated variant site (in swnv; also found in sporadic meningioma); a β-strand

Full NF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

NF2-related disorder

Also linked: NF2-related schwannomatosis hereditary neoplastic syndrome SMARCB1-related schwannomatosis

Similar variants

NF2 p.Phe96= Likely benign ★★ same residue
NF2 p.Phe96Ser Uncertain significance ★ ⚠ same residue
NF2 p.Phe96Tyr Uncertain significance ★ ⚠ same residue
NF2 p.Arg187fs Pathogenic/Likely pathogenic ★★ same condition
NF2 p.Glu445fs Pathogenic ★★ same condition
NF2 p.Phe119del Likely pathogenic ★★ same condition
NF2 p.Gln115del Uncertain significance ★★ same condition
NF2 p.Glu422del Uncertain significance ★★ 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/nf2-p-phe96del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown