BDP1 p.Thr850=
c.2550T>C · rs553166194 · VCV1318186
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.198%, mid)
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 -0.31 | GERP 1.4 |
| Overall | ||
| CADD | 1.268 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.198%
Middle Eastern · 12/6,056 alleles
Filtering AF
0.114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0896%
Overall
0.0166%
267/1,613,198 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.198% | 505 |
| Finnishnot grpmax-eligible | 0.183% | 547 |
| South Asian | 0.044% | 2,273 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,903 |
| Admixed American | 0.00669% | 14,949 |
| African / African-American | 0.00668% | 14,980 |
| European (non-Finnish) | 0.00619% | 16,162 |
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.Thr850=
- Coding
- c.2550T>C
- MANE Select
- NM_018429
- dbSNP
- rs553166194
- Type
- single nucleotide variant
- Location
- chr5:71509642 (GRCh38)
- Gene constraint
- LOEUF 0.683 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 37.23 · 13 PDB
- Residue 850
- the '9 x 55 aa repeats of g-r-r-x-i-s-p-x-e-n-g-x-e-e-v-k-p-x-x-e-m-e-t-d-l-k-x-t-g-r-e-x-x-x-r-e-k-t-x-e-x-x-d-a-x-e-e-i-d-x-d-l-e-e-t' region
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-thr850 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown