BDP1 p.Ser1634=
c.4902C>T · rs199691118 · VCV508593
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.6%, sas)
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 -0.063 | GERP 0.56 |
| Overall | ||
| CADD | 5.756 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.6%
South Asian · 1,396/87,404 alleles
Filtering AF
1.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.5%
Overall
0.094%
1,505/1,600,548 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.6% | 63 |
| Remaining individualsnot grpmax-eligible | 0.105% | 954 |
| Middle Eastern | 0.0669% | 1,495 |
| Admixed American | 0.0142% | 7,029 |
| East Asian | 0.00451% | 22,185 |
| African / African-American | 0.0027% | 37,090 |
| European (non-Finnish) | 0.00238% | 42,009 |
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.Ser1634=
- Coding
- c.4902C>T
- MANE Select
- NM_018429
- dbSNP
- rs199691118
- Type
- single nucleotide variant
- Location
- chr5:71517363 (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-ser1634 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown