NLRP3 p.Phe518=
c.1554C>T · rs2103111350 · VCV1261455
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.23 | GERP -1.2, phastCons 0.97 |
| Overall | ||
| CADD | 7.499 | PHRED · no single calibrated threshold — expert panels disagree |
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
- NLRP3
- Protein
- p.Phe518=
- Coding
- c.1554C>T
- MANE Select
- NM_001243133
- dbSNP
- rs2103111350
- Type
- single nucleotide variant
- Location
- chr1:247425003 (GRCh38)
- Gene constraint
- LOEUF 0.639 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.16 · 27 PDB
- Residue 518
- a β-strand; the nacht domain
Similar variants
- NLRP3 p.Phe518Leu Uncertain significance ★ ⚠ same residue
- AVP p.Ala19Thr Pathogenic ★★ ⚠ same type
- AVP p.Cys92Tyr Likely pathogenic ★★ same type
- AVP p.Glu108Ter Pathogenic ★★ same type
- AVP p.Gly54Arg Pathogenic ★★ same type
- AVP p.Gly96Asp Pathogenic/Likely pathogenic ★★ same type
- AVP p.Ser87Phe Pathogenic/Likely pathogenic ★★ same type
- NLRP3 p.Ala352Thr Likely pathogenic ★★ ⚠ same type
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/nlrp3-p-phe518 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown