CMPK1 p.Val149Ile
c.445G>A · VCV4230474
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0241%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.435 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.21 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.59 | unconstrained · MANE · 43 kb · p 4.9e-10 · regional, not allelic |
| Overall | ||
| CADD | 23.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0241%
African / African-American · 18/74,656 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0129%
Overall
0.0018%
29/1,607,314 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0241% | 4,148 |
| Middle Eastern | 0.0165% | 6,054 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,081 |
| Admixed American | 0.00168% | 59,416 |
| Finnishnot grpmax-eligible | 0.00157% | 63,640 |
| South Asian | 0.00111% | 90,056 |
| European (non-Finnish) | 0.000425% | 235,290 |
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.Val149Ile
- Coding
- c.445G>A
- MANE Select
- NM_016308
- Type
- single nucleotide variant
- Location
- chr1:47373081 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI 0.18 (gnomAD)
- Structure
- AlphaFold pLDDT 97.06 · 2 PDB
- Residue 149
- an α-helix
Similar variants
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- 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-val149ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown