B9D1 p.Pro92=
c.276A>C · rs996417216 · VCV1953863
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, 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 -10 | GERP -1.8 |
| Overall | ||
| CADD | 4.323 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,998 alleles
Overall
6.2e-05%
1/1,613,970 alleles · very rare
exomes 0/1,461,824 · genomes 1/152,146 · 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
- B9D1
- Protein
- p.Pro92=
- Coding
- c.276A>C
- MANE Select
- NM_015681
- dbSNP
- rs996417216
- Type
- single nucleotide variant
- Location
- chr17:19347849 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.05
- Residue 92
- the c2 b9-type domain
Similar variants
- B9D1 c.341+2T>C Pathogenic/Likely pathogenic ★★ same condition
- B9D1 p.Arg114Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- B9D1 p.Arg156Trp Pathogenic/Likely pathogenic ★★ same condition
- B9D1 c.404+5G>C Uncertain significance ★★ same condition
- B9D1 p.Ala44Val Uncertain significance ★★ ⚠ same condition
- B9D1 p.Arg101Gln Uncertain significance ★★ same condition
- B9D1 p.Arg140Gln Uncertain significance ★★ ⚠ same condition
- B9D1 p.Arg162His 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/b9d1-p-pro92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown