Is NF1 p.Pro566= (c.1698T>C) pathogenic?

NF1 p.Pro566= (c.1698T>C) is classified Benign/Likely benign in NF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-05-15). No allele count reported in gnomAD v4.1 (AN 1,606,566); Associated with neurofibromatosis type 1.

What condition is associated with NF1 p.Pro566= (c.1698T>C)?

NF1 p.Pro566= (c.1698T>C) is associated with neurofibromatosis type 1 (ClinVar).

How common is NF1 p.Pro566= (c.1698T>C) in the general population?

NF1 p.Pro566= (c.1698T>C) is no allele count reported in gnomAD v4.1 (AN 1,606,566) (gnomAD).

How is Neurofibromatosis type 1 inherited?

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

NF1 p.Pro566=

c.1698T>C · rs2144004618 · VCV1110106

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,606,566)

Conditions

neurofibromatosis type 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.31	GERP 2, phastCons 1
Overall
CADD	10.67	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,606,566). 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: NF1
Protein: p.Pro566=
Coding: c.1698T>C
MANE Select: NM_001042492
dbSNP: rs2144004618
Type: single nucleotide variant
Location: chr17:31221906 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 566: a turn

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.Pro566Ala Uncertain significance ★★ same residue
NF1 p.Pro566Leu Uncertain significance ★ same residue
NF1 p.Pro566Ser 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

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-pro566 (accessed [today's date]).

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