B9D2 p.Pro132=
c.396G>A · VCV4782553
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0296%, sas)
Conditions
2
Meckel 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 -2.5 | GERP -2.7 |
| Overall | ||
| CADD | 5.202 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0296%
South Asian · 27/91,092 alleles
Filtering AF
0.0208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.018%
Overall
0.00248%
40/1,613,824 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0296% | 3,374 |
| African / African-American | 0.00934% | 10,705 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| Admixed American | 0.00167% | 60,006 |
| European (non-Finnish) | 0.000254% | 393,335 |
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.Pro132=
- Coding
- c.396G>A
- MANE Select
- NM_030578
- Type
- single nucleotide variant
- Location
- chr19:41354832 (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-pro132 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown