Is NF1 p.His4= (c.12C>T) pathogenic?

NF1 p.His4= (c.12C>T) is classified Likely benign in NF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-12). No allele count reported in gnomAD v4.1 (AN 1,538,260); Associated with hereditary neoplastic syndrome.

What condition is associated with NF1 p.His4= (c.12C>T)?

NF1 p.His4= (c.12C>T) is associated with hereditary neoplastic syndrome, neurofibromatosis type 1 (ClinVar).

How common is NF1 p.His4= (c.12C>T) in the general population?

NF1 p.His4= (c.12C>T) is no allele count reported in gnomAD v4.1 (AN 1,538,260) (gnomAD).

NF1 p.His4=

c.12C>T · rs2143144553 · VCV1769357

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,538,260)

Conditions

hereditary neoplastic syndrome

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 2.9	GERP -0.18, phastCons 1
Overall
CADD	19.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,538,260). 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.His4=
Coding: c.12C>T
MANE Select: NM_001042492
dbSNP: rs2143144553
Type: single nucleotide variant
Location: chr17:31095321 (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-his4 (accessed [today's date]).

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