BBS12 p.Arg239=
c.715A>C · rs1800898589 · VCV1133573
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Bardet-Biedl syndrome
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 |
|---|---|---|
| Pangolin | Δ0.20 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.91 | GERP -2.4 |
| Overall | ||
| CADD | 1.109 | 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
- BBS12
- Protein
- p.Arg239=
- Coding
- c.715A>C
- MANE Select
- NM_152618
- dbSNP
- rs1800898589
- Type
- single nucleotide variant
- Location
- chr4:122742607 (GRCh38)
- Gene constraint
- LOEUF 1.419 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.92
Disease context
Bardet-Biedl syndrome — 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
- BBS12 p.Arg239Lys Uncertain significance ★★ ⚠ same residue
- BBS12 p.Arg239Trp Uncertain significance ★★ ⚠ same residue
- BBS12 p.Ala289Pro Likely pathogenic ★★ same condition
- BBS12 p.Arg214Ter Pathogenic/Likely pathogenic ★★ same condition
- BBS12 p.Arg355Ter Pathogenic ★★ same condition
- BBS12 p.Arg675Ter Pathogenic/Likely pathogenic ★★ same condition
- BBS12 p.Gln149Ter Pathogenic/Likely pathogenic ★★ same condition
- BBS12 p.Gln228Ter 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/bbs12-p-arg239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown