BAG6 p.Pro687=
c.2061T>C · VCV3388405
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.851%, 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 0.26 | GERP -0.49, phastCons 0.6 |
| Overall | ||
| CADD | 10.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.851%
Middle Eastern · 9/1,058 alleles
Filtering AF
0.745%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.711%
Overall
0.449%
1,118/248,766 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.851% | 118 |
| South Asian | 0.832% | 120 |
| Admixed American | 0.781% | 128 |
| Ashkenazi Jewishnot grpmax-eligible | 0.53% | 189 |
| Finnishnot grpmax-eligible | 0.495% | 202 |
| Remaining individualsnot grpmax-eligible | 0.434% | 230 |
| European (non-Finnish) | 0.383% | 261 |
| East Asian | 0.282% | 354 |
| African / African-American | 0.196% | 509 |
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
- BAG6
- Protein
- p.Pro687=
- Coding
- c.2061T>C
- MANE Select
- NM_001387994
- Type
- single nucleotide variant
- Location
- chr6:31642386 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 58.52 · 10 PDB
- Residue 687
- the 'disordered' region
Similar variants
- BAG6 p.Gln1137Glu Uncertain significance ★★ ⚠ same type
- BAG6 p.Ala1101Val Uncertain significance ★ ⚠ same type
- BAG6 p.Ala261Val Uncertain significance ★ ⚠ same type
- BAG6 p.Arg1027Trp Uncertain significance ★ ⚠ same type
- BAG6 p.Arg1099Trp Uncertain significance ★ ⚠ same type
- BAG6 p.Arg1107Gln Uncertain significance ★ ⚠ same type
- BAG6 p.Arg1133Gln Uncertain significance ★ ⚠ same type
- BAG6 p.Arg1150Cys 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/bag6-p-pro687 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown