BAG3 p.Arg473Ter
c.1417C>T · rs199682693 · VCV620529
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
3
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 42.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BAG3
- Protein
- p.Arg473Ter
- Coding
- c.1417C>T
- MANE Select
- NM_004281
- dbSNP
- rs199682693
- Type
- single nucleotide variant
- Location
- chr10:119676971 (GRCh38)
- Gene constraint
- LOEUF 0.538 · pLI 0.92 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.98
- Residue 473
- the bag domain
Similar variants
- BAG3 p.Arg473Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- BAG3 p.Arg121Ter Pathogenic/Likely pathogenic ★★ same condition
- BAG3 p.Arg123Ter Pathogenic/Likely pathogenic ★★ same condition
- BAG3 p.Arg309Ter Pathogenic ★★ same condition
- BAG3 p.Arg90Ter Pathogenic ★★ same condition
- BAG3 p.Gln132Ter Pathogenic ★★ same condition
- BAG3 p.Gln135Ter Pathogenic ★★ same condition
- BAG3 p.Gln244Ter Pathogenic/Likely pathogenic ★★ same condition
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/bag3-p-arg473ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown