B9D2 p.Pro103=
c.309G>A · rs201735642 · VCV697626
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00509%, nfe)
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 -16 | GERP -2.1 |
| Overall | ||
| CADD | 1.277 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00509%
European (non-Finnish) · 60/1,179,802 alleles
Filtering AF
0.00402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00362%
Overall
0.00428%
69/1,613,408 alleles · very rare
exomes 61/1,461,072 · genomes 8/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00509% | 19,663 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,824 |
| Finnishnot grpmax-eligible | 0.00471% | 21,219 |
| East Asian | 0.00446% | 22,429 |
| African / African-American | 0.00133% | 75,060 |
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.Pro103=
- Coding
- c.309G>A
- MANE Select
- NM_030578
- dbSNP
- rs201735642
- Type
- single nucleotide variant
- Location
- chr19:41354919 (GRCh38)
- Gene constraint
- LOEUF 1.518 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.79
- Residue 103
- the c2 b9-type domain
Similar variants
- B9D2 p.Pro103Ser Uncertain significance ★★ ⚠ same residue
- B9D2 p.Pro103Leu Uncertain significance ★ ⚠ same residue
- 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.Thr44Met 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-pro103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown