CMPK2 p.Thr267=
c.801G>A · VCV4822140
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0549%, sas)
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 -14 | GERP -4.2 |
| Overall | ||
| CADD | 0.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0549%
South Asian · 50/91,066 alleles
Filtering AF
0.0427%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0385%
Overall
0.00477%
77/1,613,884 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0549% | 1,821 |
| African / African-American | 0.00401% | 24,966 |
| European (non-Finnish) | 0.00195% | 51,302 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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
- CMPK2
- Protein
- p.Thr267=
- Coding
- c.801G>A
- MANE Select
- NM_207315
- Type
- single nucleotide variant
- Location
- chr2:6861375 (GRCh38)
- Gene constraint
- LOEUF 1.708 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.26
Similar variants
- CMPK2 p.Thr267Met Uncertain significance ★ ⚠ same residue
- CMPK2 p.Ala156Thr Uncertain significance ★ ⚠ same type
- CMPK2 p.Ala24Gly Uncertain significance ★ ⚠ same type
- CMPK2 p.Ala2Val Uncertain significance ★ ⚠ same type
- CMPK2 p.Ala49Ser Uncertain significance ★ ⚠ same type
- CMPK2 p.Ala49Thr Uncertain significance ★ ⚠ same type
- CMPK2 p.Ala4Ser Uncertain significance ★ ⚠ same type
- CMPK2 p.Ala4Val 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/cmpk2-p-thr267 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown