Is NF2 p.Lys124del (c.367AAG[1]) pathogenic?

NF2 p.Lys124del (c.367AAG[1]) is classified Uncertain significance in NF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-01). No gnomAD frequency available for this variant; Associated with NF2-related schwannomatosis.

What condition is associated with NF2 p.Lys124del (c.367AAG[1])?

NF2 p.Lys124del (c.367AAG[1]) is associated with NF2-related schwannomatosis (ClinVar).

How common is NF2 p.Lys124del (c.367AAG[1]) in the general population?

NF2 p.Lys124del (c.367AAG[1]) is no gnomAD frequency available for this variant (gnomAD).

How is Full NF2-related schwannomatosis inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

NF2 p.Lys124del

c.367AAG[1] · rs2518463234 · VCV2811180

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

NF2-related schwannomatosis

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 0.078	GERP -4.6, phastCons 0.17

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.Lys124del
Coding: c.367AAG[1]
MANE Select: NM_000268
dbSNP: rs2518463234
Type: Microsatellite
Location: chr22:29642205 (GRCh38)
Gene constraint: LOEUF 0.187 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 87.85 · 6 PDB
Residue 124: the ferm domain; a UniProt-annotated variant site (in sporadic meningioma); an α-helix

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

Disease context

NF2-related schwannomatosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Full NF2-related schwannomatosis (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

NF2 p.Lys124Gln Uncertain significance ★★ ⚠ same residue
NF2 p.Lys124Asn 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
NF2 p.Phe592del 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-lys124del (accessed [today's date]).

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