BAG3 p.Thr48=
c.144G>C · rs2493980100 · VCV3223769
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000171%, nfe)
Conditions
3
Cardiovascular phenotype
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 2.1 | GERP -0.12, phastCons 1 |
| Overall | ||
| CADD | 12.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000171%
European (non-Finnish) · 2/1,170,998 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000139%
2/1,441,494 alleles · very rare
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
- BAG3
- Protein
- p.Thr48=
- Coding
- c.144G>C
- MANE Select
- NM_004281
- dbSNP
- rs2493980100
- Type
- single nucleotide variant
- Location
- chr10:119651819 (GRCh38)
- Gene constraint
- LOEUF 0.538 · pLI 0.92 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.98
- Residue 48
- the ww 1 domain; the 'disordered' region
Similar variants
- BAG3 p.Thr48Ala Uncertain significance ★★ ⚠ same residue
- BAG3 p.Thr48Pro Uncertain significance ★★ ⚠ same residue
- BAG3 p.Thr48Lys Uncertain significance ★ ⚠ same residue
- BAG3 p.Thr48Met Uncertain significance ★ ⚠ 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.Arg473Ter 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-thr48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown