BDP1 p.Pro769=
c.2307T>C · rs1764470414 · VCV3045179
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00127%, nfe)
Conditions
1
BDP1-related disorder
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 3.9, phastCons 1 |
| Overall | ||
| CADD | 6.648 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00127%
European (non-Finnish) · 15/1,179,536 alleles
Filtering AF
0.000764%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00103%
15/1,461,176 alleles · very rare
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
- BDP1
- Protein
- p.Pro769=
- Coding
- c.2307T>C
- MANE Select
- NM_018429
- dbSNP
- rs1764470414
- Type
- single nucleotide variant
- Location
- chr5:71504686 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 37.23 · 13 PDB
Disease context
BDP1-related disorder
Similar variants
- BDP1 c.6413-4T>C Likely benign same condition
- BDP1 p.Gly2130= Likely benign same condition
- BDP1 p.Ile1355Met Likely benign same condition
- BDP1 p.Leu708= Likely benign same condition
- BDP1 p.Thr2432Ala Likely benign same condition
- BDP1 p.Ile1196del Uncertain significance same condition
- BDP1 p.Arg880Gly Uncertain significance ★★ ⚠ same type
- BDP1 p.Arg935Ile Uncertain significance ★★ ⚠ same type
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/bdp1-p-pro769 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown