BBS2 p.Arg539=
c.1615C>A · VCV4063758
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Bardet-Biedl syndrome 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor loss, 44 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.34 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.6 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 4.694 | PHRED · no single calibrated threshold — expert panels disagree |
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.Arg539=
- Coding
- c.1615C>A
- MANE Select
- NM_031885
- Type
- single nucleotide variant
- Location
- chr16:56498481 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49
Disease context
Bardet-Biedl syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Bardet-Biedl syndrome (Orphanet):
- Inheritance
- Autosomal recessive, Oligogenic
- Onset
- Antenatal, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Specific population)
Similar variants
- BBS2 p.Arg539Trp Uncertain significance ★★ ⚠ same residue
- BBS2 p.Arg539Gln Uncertain significance ★★ ⚠ same residue
- BBS2 c.118-1G>T Likely pathogenic ★★ same condition
- BBS2 c.118-2A>C Likely pathogenic ★★ same condition
- BBS2 c.118-2A>G Likely pathogenic ★★ same condition
- BBS2 c.1225+2T>C Likely pathogenic ★★ same condition
- BBS2 c.1225+2T>G Likely pathogenic ★★ same condition
- BBS2 c.1397+1G>A 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-arg539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown