DGKZ p.Pro596=
c.1788G>A · VCV4810495
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0204%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.255 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.9 |
| Overall | ||
| CADD | 0.697 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0204%
East Asian · 9/44,166 alleles
Filtering AF
0.0105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0079%
Overall
0.00321%
51/1,590,682 alleles · ultra-rare
exomes 40/1,438,456 · genomes 11/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0204% | 4,907 |
| Admixed American | 0.0173% | 5,782 |
| African / African-American | 0.0107% | 9,335 |
| South Asian | 0.00566% | 17,669 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,874 |
| European (non-Finnish) | 0.00153% | 65,238 |
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
- DGKZ
- Protein
- p.Pro596=
- Coding
- c.1788G>A
- MANE Select
- NM_001199267
- Type
- single nucleotide variant
- Location
- chr11:46375512 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.94 · 1 PDB
Similar variants
- DGKZ c.162-1007C>T Uncertain significance ★★ same type
- DGKZ c.162-335G>A Uncertain significance ★★ same type
- DGKZ c.162-350C>T Uncertain significance ★★ same type
- DGKZ c.162-364G>A Uncertain significance ★★ same type
- DGKZ c.162-461C>T Uncertain significance ★★ same type
- DGKZ c.162-491G>A Uncertain significance ★★ same type
- DGKZ c.162-517A>T Uncertain significance ★★ same type
- DGKZ c.162-565G>A 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/dgkz-p-pro596 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown