BDP1 p.Pro1579=
c.4737G>A · rs747494797 · VCV1316862
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0215%, nfe)
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 -1.6 | GERP -4.8 |
| Overall | ||
| CADD | 4.247 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0215%
European (non-Finnish) · 254/1,179,516 alleles
Filtering AF
0.0193%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0184%
Overall
0.017%
274/1,613,066 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0215% | 4,644 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,938 |
| Admixed American | 0.00501% | 19,973 |
| East Asian | 0.00446% | 22,427 |
| African / African-American | 0.00401% | 24,945 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,596 |
| South Asian | 0.0022% | 45,459 |
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.Pro1579=
- Coding
- c.4737G>A
- MANE Select
- NM_018429
- dbSNP
- rs747494797
- Type
- single nucleotide variant
- Location
- chr5:71516148 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 37.23 · 13 PDB
Similar variants
- BDP1 p.Arg880Gly Uncertain significance ★★ ⚠ same type
- BDP1 p.Arg935Ile Uncertain significance ★★ ⚠ same type
- BDP1 p.Asp1875Asn Uncertain significance ★★ ⚠ same type
- BDP1 p.Glu1139Val Uncertain significance ★★ ⚠ same type
- BDP1 p.Ile1035Met Uncertain significance ★★ ⚠ same type
- BDP1 p.Lys1304Glu Uncertain significance ★★ ⚠ same type
- BDP1 p.Lys354Glu Uncertain significance ★★ ⚠ same type
- BDP1 p.Pro1432Leu 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-pro1579 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown