NR0B2 p.Pro113=
c.339G>A · rs143133224 · VCV1336545
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.16%, nfe)
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 -15 | GERP -4 |
| Overall | ||
| CADD | 0.192 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.16%
European (non-Finnish) · 1,886/1,179,994 alleles
Filtering AF
0.154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.151%
Overall
0.126%
2,036/1,614,058 alleles · rare
exomes 1,881/1,461,796 · genomes 155/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.16% | 626 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Admixed American | 0.07% | 1,429 |
| African / African-American | 0.036% | 2,779 |
| Middle Eastern | 0.033% | 3,030 |
| Finnishnot grpmax-eligible | 0.025% | 3,999 |
| South Asian | 0.011% | 9,108 |
| East Asian | 0.00891% | 11,218 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- NR0B2
- Protein
- p.Pro113=
- Coding
- c.339G>A
- MANE Select
- NM_021969
- dbSNP
- rs143133224
- Type
- single nucleotide variant
- Location
- chr1:26913602 (GRCh38)
- Gene constraint
- LOEUF 1.34 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.42 · 14 PDB
- Residue 113
- the nr lbd domain
Similar variants
- NR0B2 p.Pro113Leu Uncertain significance ⚠ same residue
- NR0B2 p.Ala145Val Uncertain significance ★★ ⚠ same type
- NR0B2 p.Arg238Cys Uncertain significance ★★ ⚠ same type
- NR0B2 p.Arg54Cys Uncertain significance ★★ ⚠ same type
- NR0B2 p.Arg71Gly Uncertain significance ★★ ⚠ same type
- NR0B2 p.Arg86Trp Uncertain significance ★★ ⚠ same type
- NR0B2 p.Asp245Gly Uncertain significance ★★ ⚠ same type
- NR0B2 p.Gln84Glu 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/nr0b2-p-pro113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown