Is NF1 p.Val10= (c.30C>G) pathogenic?

NF1 p.Val10= (c.30C>G) is classified Conflicting classifications of pathogenicity in NF1 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-05-14). Very rare (popmax 0.00274%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with NF1 p.Val10= (c.30C>G)?

NF1 p.Val10= (c.30C>G) is associated with hereditary neoplastic syndrome, neurofibromatosis type 1 (ClinVar).

How common is NF1 p.Val10= (c.30C>G) in the general population?

NF1 p.Val10= (c.30C>G) is very rare (popmax 0.00274%, afr) (gnomAD).

NF1 p.Val10=

c.30C>G · rs1033348008 · VCV759525

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00274%, afr)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.3	GERP 0.8, phastCons 1
Overall
CADD	19.54	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00274% African / African-American · 2/72,984 alleles

Filtering AF 0.000455% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00017%

Overall 0.00013% 2/1,539,698 alleles · very rare exomes 1/1,387,700 · genomes 1/151,998 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: NF1
Protein: p.Val10=
Coding: c.30C>G
MANE Select: NM_001042492
dbSNP: rs1033348008
Type: single nucleotide variant
Location: chr17:31095339 (GRCh38)

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: neurofibromatosis type 1

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-val10 (accessed [today's date]).

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