DGKD p.Pro597=
c.1791G>A · rs1294563312 · VCV3040094
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Conditions
1
DGKD-related disorder
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 -8.8 | GERP -3.1 |
| Overall | ||
| CADD | 0.566 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,880 alleles
Filtering AF
0.00334%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00302%
Overall
0.00353%
57/1,613,216 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,440 |
| European (non-Finnish) | 0.00432% | 23,130 |
| Admixed American | 0.00333% | 30,006 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,470 |
| African / African-American | 0.00133% | 74,926 |
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
- DGKD
- Protein
- p.Pro597=
- Coding
- c.1791G>A
- MANE Select
- NM_152879
- dbSNP
- rs1294563312
- Type
- single nucleotide variant
- Location
- chr2:233449279 (GRCh38)
- Gene constraint
- LOEUF 0.547 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.02 · 2 PDB
Disease context
DGKD-related disorder
Similar variants
- DGKD p.Pro597Leu Uncertain significance ★ ⚠ same residue
- DGKD p.Ala847= Likely benign same condition
- DGKD p.Asn1034Ser Benign same condition
- DGKD p.Glu971Lys Likely benign same condition
- DGKD p.Gly1099Cys Likely benign same condition
- DGKD p.Leu891= Benign same condition
- DGKD p.Ser498= Benign same condition
- DGKD p.Ser529= Likely benign same condition
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/dgkd-p-pro597 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown