CHKB p.Pro208=
c.624T>G · rs1603443728 · VCV746914
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 -0.44 | GERP -4.7, phastCons 0.006 |
| Overall | ||
| CADD | 0.513 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,000 alleles
Overall
6.2e-05%
1/1,613,802 alleles · very rare
exomes 1/1,461,626 · genomes 0/152,176 · joint denominator
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
- CHKB
- Protein
- p.Pro208=
- Coding
- c.624T>G
- MANE Select
- NM_005198
- dbSNP
- rs1603443728
- Type
- single nucleotide variant
- Location
- chr22:50580618 (GRCh38)
- Gene constraint
- LOEUF 1.015 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.54 · 3 PDB
- Residue 208
- a UniProt-annotated variant site (in mdcmc; loss of choline kinase activity; decreased amount of phosphatidylcholine in patients cells); a UniProt-annotated variant site (in mdcmc)
Similar variants
- CHKB p.Gln51Ter Pathogenic/Likely pathogenic ★★ same type
- CHKB c.*208T>G Uncertain significance ★★ same type
- CHKB p.Ala361Val Uncertain significance ★★ ⚠ same type
- CHKB p.Arg344Trp Uncertain significance ★★ ⚠ same type
- CHKB p.Arg62Cys Uncertain significance ★★ ⚠ same type
- CHKB p.Gln309Glu Uncertain significance ★★ same type
- CHKB p.Glu214Asp Uncertain significance ★★ ⚠ same type
- CHKB p.Glu336Lys 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/chkb-p-pro208 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown