BDP1 p.Pro1963=
c.5889G>A · rs35126870 · VCV515795
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.79%, afr)
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 0.29 | GERP -3.6, phastCons 0.001 |
| Overall | ||
| CADD | 6.503 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.79%
African / African-American · 1,340/74,978 alleles
Filtering AF
1.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.68%
Overall
0.115%
1,859/1,612,610 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.79% | 56 |
| Middle Eastern | 0.334% | 299 |
| Remaining individualsnot grpmax-eligible | 0.234% | 428 |
| South Asian | 0.13% | 769 |
| Admixed American | 0.127% | 788 |
| European (non-Finnish) | 0.0134% | 7,464 |
| East Asian | 0.00223% | 44,772 |
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.Pro1963=
- Coding
- c.5889G>A
- MANE Select
- NM_018429
- dbSNP
- rs35126870
- Type
- single nucleotide variant
- Location
- chr5:71532424 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 37.23 · 13 PDB
Similar variants
- BDP1 p.Pro1963Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro1963 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown