NF1 p.Phe231=
c.693T>C · rs876660028 · VCV232853
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.5e-05%, nfe)
Conditions
1
hereditary neoplastic syndrome
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 6.1 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,176,296 alleles
Overall
6.21e-05%
1/1,609,696 alleles · very rare
exomes 1/1,457,680 · genomes 0/152,016 · 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.Phe231=
- Coding
- c.693T>C
- MANE Select
- NM_001042492
- dbSNP
- rs876660028
- Type
- single nucleotide variant
- Location
- chr17:31181748 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 231
- an α-helix
Similar variants
- NF1 p.Phe231Val Uncertain significance ★ ⚠ same residue
- NF1 c.1062+2T>C Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1062+3A>G Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1063-13G>A Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1063-1G>A Pathogenic/Likely pathogenic ★★ same condition
- NF1 c.1063-2A>C Pathogenic ★★ same condition
- NF1 c.1063-2A>G Pathogenic ★★ same condition
- NF1 c.1185+1G>A 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-phe231 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown