BAZ2A p.Pro1336=
c.4008G>A · rs372432526 · VCV2643099
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00458%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.335 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.35 | GERP -1.7, phastCons 0.32 |
| Overall | ||
| CADD | 15.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00458%
European (non-Finnish) · 54/1,179,824 alleles
Filtering AF
0.00358%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00321%
Overall
0.00353%
57/1,613,664 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00458% | 21,849 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| Finnishnot grpmax-eligible | 0.00157% | 63,890 |
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
- BAZ2A
- Protein
- p.Pro1336=
- Coding
- c.4008G>A
- MANE Select
- NM_001300905
- dbSNP
- rs372432526
- Type
- single nucleotide variant
- Location
- chr12:56601609 (GRCh38)
- Gene constraint
- LOEUF 0.226 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.27 · 67 PDB
- Residue 1336
- the 'disordered' region
Similar variants
- BAZ2A p.Ala1061Pro Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1111Ser Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1160Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1223Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1229Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala142Thr Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala1770Val Uncertain significance ★ ⚠ same type
- BAZ2A p.Ala17Val 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/baz2a-p-pro1336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown