BDH2 p.Thr182=
c.546G>A · rs60495707 · VCV784042
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.31%, 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 -0.76 | GERP -1.4 |
| Overall | ||
| CADD | 10.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.31%
African / African-American · 983/74,976 alleles
Filtering AF
1.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.22%
Overall
0.19%
3,056/1,612,536 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.31% | 76 |
| Middle Eastern | 0.792% | 126 |
| Admixed American | 0.591% | 169 |
| Remaining individualsnot grpmax-eligible | 0.328% | 305 |
| Ashkenazi Jewishnot grpmax-eligible | 0.162% | 617 |
| European (non-Finnish) | 0.118% | 849 |
| South Asian | 0.0286% | 3,502 |
| Finnishnot grpmax-eligible | 0.0047% | 21,287 |
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
- BDH2
- Protein
- p.Thr182=
- Coding
- c.546G>A
- MANE Select
- NM_020139
- dbSNP
- rs60495707
- Type
- single nucleotide variant
- Location
- chr4:103082916 (GRCh38)
- Gene constraint
- LOEUF 1.253 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.46 · 1 PDB
- Residue 182
- a binding site
Similar variants
- BDH2 p.Ala14Thr Uncertain significance ★ ⚠ same type
- BDH2 p.Ala23Pro Uncertain significance ★ ⚠ same type
- BDH2 p.Ala27Val Uncertain significance ★ ⚠ same type
- BDH2 p.Arg199Trp Uncertain significance ★ ⚠ same type
- BDH2 p.Arg3Gln Uncertain significance ★ ⚠ same type
- BDH2 p.Arg55Cys Uncertain significance ★ ⚠ same type
- BDH2 p.Arg55His Uncertain significance ★ ⚠ same type
- BDH2 p.Asn103His 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/bdh2-p-thr182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown