NOD2 p.Arg1007=
c.3021G>A · VCV4790246
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
Conditions
2
Regional enteritis
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 3.7 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 2.603 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,056 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.000205%
3/1,461,510 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,028 |
| European (non-Finnish) | 8.48e-05% | 1,179,720 |
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.Arg1007=
- Coding
- c.3021G>A
- MANE Select
- NM_001370466
- Type
- single nucleotide variant
- Location
- chr16:50731798 (GRCh38)
- Gene constraint
- LOEUF 1.033 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.76
- Residue 1007
- a UniProt-annotated variant site (in ibd1; abolished nf-kappa-b activation in response to muramyl dipeptide stimulation; decreased localization to the cell membrane)
Similar variants
- NOD2 p.Arg307Gln Pathogenic ★★ ⚠ same condition
- NOD2 p.Arg307Trp Pathogenic ★★ ⚠ same condition
- NOD2 p.Arg560Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- NOD2 p.Met486Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- NOD2 c.2550-2A>G Uncertain significance ★★ same condition
- NOD2 c.2717+2T>A Uncertain significance ★★ same condition
- NOD2 c.2885+6G>T Uncertain significance ★★ same condition
- NOD2 c.459+1G>A Uncertain significance ★★ 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/nod2-p-arg1007 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown