CKM p.Pro21=
c.63C>T · rs138224618 · VCV2650098
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.323%, nfe)
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 -20 | GERP -4.9 |
| Overall | ||
| CADD | 0.043 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.323%
European (non-Finnish) · 3,806/1,180,020 alleles
Filtering AF
0.314%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.31%
Overall
0.247%
3,983/1,614,190 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.323% | 310 |
| Remaining individualsnot grpmax-eligible | 0.131% | 762 |
| African / African-American | 0.0586% | 1,706 |
| Finnishnot grpmax-eligible | 0.05% | 2,001 |
| Admixed American | 0.0283% | 3,531 |
| East Asian | 0.00223% | 44,880 |
| South Asian | 0.0011% | 91,084 |
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
- CKM
- Protein
- p.Pro21=
- Coding
- c.63C>T
- MANE Select
- NM_001824
- dbSNP
- rs138224618
- Type
- single nucleotide variant
- Location
- chr19:45319651 (GRCh38)
- Gene constraint
- LOEUF 1.088 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.92 · 2 PDB
- Residue 21
- the phosphagen kinase n-terminal domain
Similar variants
- CKM p.Leu127Val Uncertain significance ★★ ⚠ same type
- CKM p.Pro91Ser Uncertain significance ★★ ⚠ same type
- CKM p.Arg251Pro Likely benign ★★ ⚠ same type
- CKM p.Ala214Thr Uncertain significance ★ ⚠ same type
- CKM p.Ala267Asp Uncertain significance ★ ⚠ same type
- CKM p.Ala267Val Uncertain significance ★ ⚠ same type
- CKM p.Arg135Gly Uncertain significance ★ ⚠ same type
- CKM p.Arg135His 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/ckm-p-pro21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown