CAMK2B p.Ser487=
c.1461C>T · rs1178438857 · VCV2982128
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00238%, eas)
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 0.12 | GERP 0.65, phastCons 0.001 |
| Overall | ||
| CADD | 5.865 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00238%
East Asian · 1/42,062 alleles
Overall
0.00131%
2/152,136 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00238% | 42,062 |
| South Asian | 0.00135% | 74,234 |
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
- CAMK2B
- Protein
- p.Ser487=
- Coding
- c.1461C>T
- MANE Select
- NM_001220
- dbSNP
- rs1178438857
- Type
- single nucleotide variant
- Location
- chr7:44228803 (GRCh38)
- Gene constraint
- LOEUF 0.45 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 72.35 · 4 PDB
- Residue 487
- a UniProt-annotated variant site (in mrd54); the 'disordered' region
Similar variants
- CAMK2B p.Ser487Ala Uncertain significance ★ ⚠ same residue
- CAMK2B c.903+2T>C Likely pathogenic ★★ same type
- CAMK2B p.Arg29Ter Pathogenic/Likely pathogenic ★★ same type
- CAMK2B p.Glu110Lys Pathogenic ★★ same type
- CAMK2B p.Glu237Lys Pathogenic ★★ same type
- CAMK2B p.Lys301Glu Pathogenic/Likely pathogenic ★★ same type
- CAMK2B p.Pro139Leu Pathogenic/Likely pathogenic ★★ same type
- CAMK2B c.1059+1G>A 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/camk2b-p-ser487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown