BDP1 p.Thr1328=
c.3984C>A · rs371188829 · VCV1317507
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0847%, eas)
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 -0.62 | GERP 2 |
| Overall | ||
| CADD | 5.233 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0847%
East Asian · 38/44,884 alleles
Filtering AF
0.0634%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.056%
Overall
0.0026%
42/1,614,018 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0847% | 1,181 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,830 |
| Admixed American | 0.00167% | 59,992 |
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.Thr1328=
- Coding
- c.3984C>A
- MANE Select
- NM_018429
- dbSNP
- rs371188829
- Type
- single nucleotide variant
- Location
- chr5:71511076 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 37.23 · 13 PDB
- Residue 1328
- the 'disordered' region
Similar variants
- BDP1 p.Thr1328Ala 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-thr1328 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown