BBS2 p.Glu426Ter
c.1276G>T · rs2543707803 · VCV3028359
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 11 of 17 |
| Splicing | ||
| SpliceAI | Δ0.28 | acceptor loss · deltas |
| Pangolin | Δ0.39 | loss · gain 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 38.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BBS2
- Protein
- p.Glu426Ter
- Coding
- c.1276G>T
- MANE Select
- NM_031885
- dbSNP
- rs2543707803
- Type
- single nucleotide variant
- Location
- chr16:56500975 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49
Similar variants
- BBS2 c.941-2A>C Pathogenic ★★ same condition
- BBS2 p.Arg189Ter Pathogenic ★★ same condition
- BBS2 p.Arg216Ter Pathogenic ★★ same condition
- BBS2 p.Arg234Ter Pathogenic ★★ same condition
- BBS2 p.Arg272Ter Pathogenic ★★ same condition
- BBS2 p.Arg275Ter Pathogenic/Likely pathogenic ★★ same condition
- BBS2 p.Arg315Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- BBS2 p.Arg315Trp Pathogenic/Likely pathogenic ★★ ⚠ 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/bbs2-p-glu426ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown