B9D2 p.Gly129=
c.387T>C · VCV3755795
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Conditions
2
Joubert 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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.9 | GERP -2.7 |
| Overall | ||
| CADD | 2.469 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,026 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000479%
7/1,461,606 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,009 |
| European (non-Finnish) | 0.000339% | 294,992 |
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
- B9D2
- Protein
- p.Gly129=
- Coding
- c.387T>C
- MANE Select
- NM_030578
- Type
- single nucleotide variant
- Location
- chr19:41354841 (GRCh38)
- Gene constraint
- LOEUF 1.518 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.79
Similar variants
- B9D2 p.Gly155Ser Pathogenic/Likely pathogenic ★★ same condition
- B9D2 p.Pro74Ser Pathogenic/Likely pathogenic ★★ same condition
- B9D2 p.Arg88Cys Uncertain significance ★★ ⚠ same condition
- B9D2 p.Gln50His Uncertain significance ★★ ⚠ same condition
- B9D2 p.Gly162Cys Uncertain significance ★★ ⚠ same condition
- B9D2 p.Pro103Ser Uncertain significance ★★ ⚠ same condition
- B9D2 p.Thr44Met Uncertain significance ★★ ⚠ same condition
- B9D2 p.Val39Met Uncertain significance ★★ ⚠ 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/b9d2-p-gly129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown