CALB2 p.Ser212=
c.636C>T · rs779846737 · VCV3136636
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.376 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.7 |
| Overall | ||
| CADD | 11.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,018 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.000547%
8/1,461,760 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,574 |
| European (non-Finnish) | 8.47e-05% | 1,179,958 |
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
- CALB2
- Protein
- p.Ser212=
- Coding
- c.636C>T
- MANE Select
- NM_001740
- dbSNP
- rs779846737
- Type
- single nucleotide variant
- Location
- chr16:71385585 (GRCh38)
- Gene constraint
- LOEUF 0.958 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.29
- Residue 212
- a binding site; the ef-hand 5 domain
Similar variants
- CALB2 p.Ala115Val Uncertain significance ★ ⚠ same type
- CALB2 p.Ala129Val Uncertain significance ★ ⚠ same type
- CALB2 p.Arg145Gln Uncertain significance ★ ⚠ same type
- CALB2 p.Arg145Leu Uncertain significance ★ ⚠ same type
- CALB2 p.Arg161Gln Uncertain significance ★ ⚠ same type
- CALB2 p.Arg258Cys Uncertain significance ★ ⚠ same type
- CALB2 p.Asn231Ser Uncertain significance ★ ⚠ same type
- CALB2 p.Asn236Ser 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/calb2-p-ser212 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown