NR2E3 p.Pro149=
c.447C>T · rs757833321 · VCV1122060
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00401%, 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 -3.7 | GERP -3 |
| Overall | ||
| CADD | 0.699 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
European (non-Finnish) · 46/1,148,522 alleles
Filtering AF
0.00307%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00275%
Overall
0.00322%
50/1,553,136 alleles · very rare
exomes 48/1,400,978 · genomes 2/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00401% | 24,968 |
| Admixed American | 0.00391% | 25,586 |
| Remaining individualsnot grpmax-eligible | 0.00332% | 30,098 |
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
- NR2E3
- Protein
- p.Pro149=
- Coding
- c.447C>T
- MANE Select
- NM_014249
- dbSNP
- rs757833321
- Type
- single nucleotide variant
- Location
- chr15:71812052 (GRCh38)
- Gene constraint
- LOEUF 1.47 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.59 · 1 PDB
- Residue 149
- the 'disordered' region
Similar variants
- NR2E3 c.118+1G>T Likely pathogenic ★★ same type
- NR2E3 c.119-2A>C Pathogenic/Likely pathogenic ★★ same type
- NR2E3 c.119-2A>G Pathogenic ★★ same type
- NR2E3 c.119-2A>T Pathogenic/Likely pathogenic ★★ same type
- NR2E3 c.246-1G>C Likely pathogenic ★★ same type
- NR2E3 c.349+5G>C Pathogenic/Likely pathogenic ★★ same type
- NR2E3 c.748-1G>A Likely pathogenic ★★ same type
- NR2E3 p.Ala102Asp Pathogenic/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/nr2e3-p-pro149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown