CMPK1 p.Ser147Pro
c.439T>C · rs1243728313 · VCV2357608
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.413 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.35 | donor loss, 4 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -0.54, phastCons 1 |
| Regional constraint | o/e 0.59 | unconstrained · MANE · 43 kb · p 4.9e-10 · regional, not allelic |
| Overall | ||
| CADD | 18.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
Admixed American · 7/59,556 alleles
Filtering AF
0.00547%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00383%
Overall
0.000481%
7/1,456,706 alleles · ultra-rare
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.Ser147Pro
- Coding
- c.439T>C
- MANE Select
- NM_016308
- dbSNP
- rs1243728313
- Type
- single nucleotide variant
- Location
- chr1:47373075 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI 0.18 (gnomAD)
- Structure
- AlphaFold pLDDT 97.06 · 2 PDB
- Residue 147
- an α-helix
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-ser147pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown