NBEAL2 p.Pro668=
c.2004C>G · VCV4711646
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.241 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.1 |
| Overall | ||
| CADD | 0.365 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,086 alleles
Overall
6.2e-05%
1/1,613,850 alleles · very rare
exomes 1/1,461,558 · genomes 0/152,292 · 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
- NBEAL2
- Protein
- p.Pro668=
- Coding
- c.2004C>G
- MANE Select
- NM_015175
- Type
- single nucleotide variant
- Location
- chr3:46995819 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI <0.01 (gnomAD)
Similar variants
- NBEAL2 c.4485-1G>A Pathogenic/Likely pathogenic ★★ same type
- NBEAL2 c.4485-1G>T Pathogenic/Likely pathogenic ★★ same type
- NBEAL2 p.Arg2120Gln Likely pathogenic ★★ same type
- NBEAL2 p.Arg597Ter Pathogenic ★★ same type
- NBEAL2 p.Glu1361Ter Pathogenic ★★ same type
- NBEAL2 c.2557-5C>G Uncertain significance ★★ same type
- NBEAL2 c.5459+8G>A Uncertain significance ★★ same type
- NBEAL2 c.*267G>C 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/nbeal2-p-pro668 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown