Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.44%, afr)
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 -3.1 |
| Overall | ||
| CADD | 0.518 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.44%
African / African-American · 1,771/72,450 alleles
Filtering AF
2.35%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.31%
Overall
0.132%
2,037/1,544,632 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.44% | 41 |
| Middle Eastern | 0.28% | 358 |
| Admixed American | 0.182% | 551 |
| Remaining individualsnot grpmax-eligible | 0.175% | 571 |
| South Asian | 0.00504% | 19,839 |
| European (non-Finnish) | 0.00479% | 20,871 |
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
- CAMK4
- Protein
- p.Ala458=
- Coding
- c.1374T>G
- MANE Select
- NM_001744
- dbSNP
- rs6886469
- Type
- single nucleotide variant
- Location
- chr5:111484418 (GRCh38)
- Gene constraint
- LOEUF 1.098 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 72.09 · 1 PDB
- Residue 458
- the 'disordered' region
Similar variants
- CAMK4 p.Gln314Ter Uncertain significance ★★ same type
- CAMK4 c.981+1G>A Pathogenic ★ same type
- CAMK4 p.Met310Thr Pathogenic ★ same type
- CAMK4 c.303+1G>C Uncertain significance ★ same type
- CAMK4 c.303+2T>C Uncertain significance ★ same type
- CAMK4 p.Ala153Gly Uncertain significance ★ ⚠ same type
- CAMK4 p.Ala179Val Uncertain significance ★ ⚠ same type
- CAMK4 p.Ala217Val 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/camk4-p-ala458 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown