NOD2 p.Arg153=
c.459G>A · VCV4929803
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.74 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.53 | loss · gain 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 21.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,532 alleles
Overall
6.23e-05%
1/1,604,036 alleles · very rare
exomes 1/1,451,762 · genomes 0/152,274 · 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
- NOD2
- Protein
- p.Arg153=
- Coding
- c.459G>A
- MANE Select
- NM_001370466
- Type
- single nucleotide variant
- Location
- chr16:50699954 (GRCh38)
- Gene constraint
- LOEUF 1.033 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.76
- Residue 153
- the card 2 domain
Similar variants
- NOD2 p.Arg153Lys Uncertain significance ★ ⚠ same residue
- NOD2 p.Arg307Gln Pathogenic ★★ ⚠ same type
- NOD2 p.Arg307Trp Pathogenic ★★ ⚠ same type
- NOD2 p.Arg560Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- NOD2 p.Met486Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- NOD2 c.2550-2A>G Uncertain significance ★★ same type
- NOD2 c.2717+2T>A Uncertain significance ★★ same type
- NOD2 c.2885+6G>T Uncertain significance ★★ 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/nod2-p-arg153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown