CAMK2B p.Pro489=
c.1467G>A · rs536589861 · VCV1515939
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0105%, amr)
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 -3.7 | GERP -3.6 |
| Overall | ||
| CADD | 5.909 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0105%
Admixed American · 4/38,108 alleles
Filtering AF
0.00358%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00246%
Overall
0.00128%
19/1,485,430 alleles · ultra-rare
exomes 14/1,333,270 · genomes 5/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0105% | 9,527 |
| South Asian | 0.00832% | 12,024 |
| Remaining individualsnot grpmax-eligible | 0.00176% | 56,978 |
| African / African-American | 0.00141% | 70,684 |
| European (non-Finnish) | 0.000624% | 160,138 |
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.Pro489=
- Coding
- c.1467G>A
- MANE Select
- NM_001220
- dbSNP
- rs536589861
- Type
- single nucleotide variant
- Location
- chr7:44228797 (GRCh38)
- Gene constraint
- LOEUF 0.45 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 72.35 · 4 PDB
- Residue 489
- a UniProt-annotated variant site (in mrd54); a UniProt-annotated variant site (in a colorectal adenocarcinoma sample; somatic mutation); the 'disordered' region
Similar variants
- CAMK2B p.Pro489Leu Conflicting classifications of pathogenicity ★ ⚠ 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-pro489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown