CMPK1 p.Ser29Phe
c.86C>T · VCV4654718
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00243%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.07 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.32 | GERP 0.63 |
| Regional constraint | o/e 1.31 | unconstrained · MANE · 100 bp · p 0.038 · regional, not allelic |
| Overall | ||
| CADD | 12.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00243%
East Asian · 1/41,124 alleles
Overall
0.000257%
4/1,556,080 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00243% | 41,124 |
| African / African-American | 0.00139% | 72,146 |
| South Asian | 0.00118% | 84,524 |
| European (non-Finnish) | 8.69e-05% | 1,151,368 |
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
- CMPK1
- Protein
- p.Ser29Phe
- Coding
- c.86C>T
- MANE Select
- NM_016308
- Type
- single nucleotide variant
- Location
- chr1:47334031 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI 0.18 (gnomAD)
- Structure
- AlphaFold pLDDT 97.06 · 2 PDB
Similar variants
- CMPK1 p.Arg54Leu Uncertain significance ★ same type
- CMPK1 p.Arg6Leu Uncertain significance ★ same type
- CMPK1 p.Asn156Ser Uncertain significance ★ same type
- CMPK1 p.Glu178Lys Uncertain significance ★ same type
- CMPK1 p.Gly43Cys Uncertain significance ★ same type
- CMPK1 p.Ile207Val Uncertain significance ★ same type
- CMPK1 p.Leu10Phe Uncertain significance ★ same type
- CMPK1 p.Pro24Thr 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/cmpk1-p-ser29phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown