Is NF1 p.Leu2139Phe (c.6415C>T) pathogenic?

NF1 p.Leu2139Phe (c.6415C>T) is classified Uncertain significance in NF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-16). AlphaMissense: ambiguous (0.4756); Absent from gnomAD v4.1; Associated with neurofibromatosis type 1.

What condition is associated with NF1 p.Leu2139Phe (c.6415C>T)?

NF1 p.Leu2139Phe (c.6415C>T) is associated with neurofibromatosis type 1 (ClinVar).

How common is NF1 p.Leu2139Phe (c.6415C>T) in the general population?

NF1 p.Leu2139Phe (c.6415C>T) is absent from gnomAD v4.1 (gnomAD).

How is Neurofibromatosis type 1 inherited?

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

What do computational predictors say about NF1 p.Leu2139Phe (c.6415C>T)?

AlphaMissense predicts ambiguous (score 0.4756) — an in-silico prediction, not a clinical call.

NF1 p.Leu2139Phe

c.6415C>T · rs2508750187 · VCV1716489

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4756 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

neurofibromatosis type 1

Computational evidence

Protein change
AlphaMissense	0.4756	ambiguous
REVEL	0.509	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Regional constraint	o/e 0.41	unconstrained · MANE · 9,812 bp · p 2.1e-34 · regional, not allelic
Overall
CADD	25.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: NF1
Protein: p.Leu2139Phe
Coding: c.6415C>T
MANE Select: NM_001042492
dbSNP: rs2508750187
Type: single nucleotide variant
Location: chr17:31336902 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2139: a β-strand

Full NF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurofibromatosis type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Neurofibromatosis type 1 (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal
Prevalence: 1-5 / 10 000 (United Kingdom)

Similar variants

NF1 p.Leu2139Pro Uncertain significance ★ same residue
NF1 p.Leu2139Ile Uncertain significance ★ same residue
NF1 c.1062+1G>A Pathogenic/Likely pathogenic ★★ same condition
NF1 c.1062+1G>C Pathogenic ★★ same condition
NF1 c.1062+2T>A Pathogenic/Likely pathogenic ★★ same condition
NF1 c.1062+2T>C Pathogenic/Likely pathogenic ★★ same condition
NF1 c.1062+3A>G Pathogenic/Likely pathogenic ★★ same condition
NF1 c.1062+3A>T 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-leu2139phe (accessed [today's date]).

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